mcdoe: MultiplexCrisprDOE.jl annotate

annotate MultiplexCrisprDOE.jl @ 1:4a5c94d1d8bb draft

planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2

author	padge
date	Wed, 31 Aug 2022 12:13:10 +0000
parents	cc0957c46408
children

rev	line source
0 cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	2 gRNA_frequency_distribution(m,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	3 sd,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	4 l,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	5 u,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	6 n_gRNA_total;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	7 normalize = true,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	8 visualize = false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	9
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	10 Generates vector with frequencies in the combinatorial gRNA/Cas9 construct library for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	11
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	12 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	13 m: the average abundance of the gRNAs (in terms of absolute or relative frequency)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	14 sd: the standard deviation on the gRNA abundances (in terms of absolute or relative frequency)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	15 l: minimal gRNA abundance (in terms of absolute or relative frequency)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	16 u: maximal gRNA abundance (in terms of absolute or relative frequency)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	17 n_gRNA_total: the total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	18 normalize: if set to "true", the gRNA abundances (absolute frequencies) are converted into relative frequencies
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	19 visualize: if set to "true", a histogram of all gRNA abundances is plotted
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	20
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	21 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	22 p_gRNA_freq: vector with frequencies for all gRNAs in the construct library
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	23 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	24 function gRNA_frequency_distribution(m,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	25 sd,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	26 l,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	27 u,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	28 n_gRNA_total;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	29 normalize = true,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	30 visualize = false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	31
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	32 d_gRNA_freq = truncated(Normal(m, sd), l, u) # gRNA frequency distribution
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	33 p_gRNA_freq = collect(rand(d_gRNA_freq, n_gRNA_total)) # sample gRNA frequencies from distribution
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	34
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	35 if normalize # convert into relative frequencies
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	36 p_gRNA_freq /= sum(p_gRNA_freq)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	37 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	38
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	39 if visualize
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	40 return histogram(p_gRNA_freq, label="",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	41 xlabel="Number of reads per gRNA",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	42 linecolor="white",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	43 normalize=:probability,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	44 xtickfontsize=10,ytickfontsize=10,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	45 color=:mediumturquoise, size=(600,350), bins = 25,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	46 ylabel="Relative frequency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	47 title="gRNA frequency distribution")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	48 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	49 return p_gRNA_freq
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	50 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	51 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	52
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	53 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	54 gRNA_edit_distribution(f_act,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	55 ϵ_edit_act,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	56 ϵ_edit_inact,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	57 sd_act,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	58 n_gRNA_total;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	59 visualize = false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	60
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	61 Generates vector with genome editing efficiencies for all the gRNAs in the experiment.
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	62
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	63 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	64 f_act: fraction of all gRNAs that is active
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	65 ϵ_edit_act: Average genome editing efficiency for active gRNAs - mean of the genome editing efficiency distribution for active gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	66 ϵ_edit_inact: Average genome editing efficiency for inactive gRNAs - mean of the genome editing efficiency distribution for inactive gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	67 sd_act: standard deviation of the genome editing efficiency distributions for active and inactive gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	68 n_gRNA_total: the total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	69 visualize: if set to "true", a histogram of all genome editing efficiency is plotted
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	70
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	71 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	72 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	73 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	74 function gRNA_edit_distribution(f_act, ϵ_edit_act, ϵ_edit_inact, sd_act, n_gRNA_total; visualize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	75 d_act = Binomial(1, f_act) # there is a probability f_act that a gRNA is active
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	76 d_high_act = truncated(Normal(ϵ_edit_act, sd_act), 0.01, 1) # average genome editing efficiency for active gRNAs is equal to ϵ_edit_act
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	77 d_low_act = truncated(Normal(ϵ_edit_inact, sd_act), 0.01, 1) # average genome editing efficiency for inactive gRNAs is equal to ϵ_edit_inact
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	78 p_gRNA_edit = zeros(n_gRNA_total) # initialize vector with genome editing efficiencies for gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	79
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	80 for i in 1:n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	81 if rand(d_act, 1) == [1] # gRNA is active
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	82 p_gRNA_edit[i] = rand(d_high_act, 1)[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	83 else # gRNA is inactive
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	84 p_gRNA_edit[i] = rand(d_low_act, 1)[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	85 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	86 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	87
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	88 if visualize
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	89 return histogram(p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	90 normalize = :probability,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	91 linecolor = "white",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	92 label="",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	93 color=:turquoise4,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	94 xtickfontsize=10,ytickfontsize=10, xlim = (0, 1),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	95 xticks=(0:0.1:1),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	96 bins = 150,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	97 xlabel="gRNA editing efficiency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	98 ylabel="Relative frequency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	99 title="gRNA genome editing effiency distribution")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	100
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	101 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	102 return p_gRNA_edit
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	103 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	104 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	105
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	106 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	107 simulate_Nₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	108 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	109 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	110 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	111 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	112 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	113 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	114 iter = 500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	115
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	116 Computes the expected value and the standard deviation of the minimal plant library size for full coverage of all single gene knockouts (E[Nx,1] and σ[Nx,1]) using simulation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	117
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	118 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	119 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	120 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	121 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	122 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	123 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	124 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	125 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	126 iter: number of CRISPR/Cas experiments that are simulated to obtain E[Nₓ₁] and σ[Nₓ₁]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	127
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	128 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	129 E_Nₓ₁: expected value of the plant library size for full coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	130 sd_Nₓ₁: standard deviation on the plant library size for full coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	131 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	132 function simulate_Nₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	133 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	134 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	135 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	136 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	137 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	138 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	139 iter = 500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	140
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	141 @assert x * g == n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	142 Nₓ₁_vec = [] #stores number of plants to reach full coverage for each simulated experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	143 for i in 1:iter
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	144 genes_vec = [] # Initialize vector to store single gene knockouts that are observed in plants
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	145 Nₓ₁ = 0
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	146 while genes_vec != collect(1:x) # check if all possible single gene knockouts are present: if no full coverage, sample an additional plant
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	147 Nₓ₁ += 1 # count how many plants must be sampled to observe all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	148
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	149 # sample combinatorial gRNA/Cas9 construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	150 gRNA_indices_construct = findall((rand(Multinomial(r, p_gRNA_freq))) .!= 0)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	151
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	152 # execute mutations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	153 gRNA_indices_mutations = [gRNA for gRNA in gRNA_indices_construct if rand(Binomial(1, p_gRNA_edit[gRNA])) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	154
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	155 # effective gene knockout (loss-of-function) ?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	156 gRNA_indices_KO = [gRNA for gRNA in gRNA_indices_mutations if rand(Binomial(1, ϵ_KO)) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	157
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	158 # which genes are knocked out?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	159 genes_indices_KO = Int.(ceil.(gRNA_indices_KO / g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	160 append!(genes_vec, genes_indices_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	161
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	162 # update vector with observed gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	163 genes_vec = Int.(sort(unique(genes_vec)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	164 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	165 push!(Nₓ₁_vec, Nₓ₁) # add plant library size for full coverage of current experiment to vector
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	166 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	167
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	168 # Calculate expected value and standard deviation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	169 E_Nₓ₁ = mean(Nₓ₁_vec);
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	170 sd_Nₓ₁ = std(Nₓ₁_vec)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	171
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	172 return E_Nₓ₁, sd_Nₓ₁
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	173 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	174
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	175
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	176 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	177 BioCCP_Nₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	178 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	179 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	180 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	181 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	182 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	183 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	184
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	185 Computes the expected value and the standard deviation of the minimal plant library size for
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	186 full coverage of all single gene knockouts (E[Nx,1] and σ[Nx,1]) using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	187
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	188 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	189 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	190 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	191 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	192 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	193 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	194 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	195 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	196
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	197 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	198 E_Nₓ₁ : expected value of the plant library size for full coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	199 sd_Nₓ₁ : standard deviation on the plant library size for full coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	200 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	201 function BioCCP_Nₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	202 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	203 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	204 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	205 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	206 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	207 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	208
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	209 # prepare input for BioCCP functions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	210 p_gRNAs = p_gRNA_freq .* p_gRNA_edit * ϵ_KO # calculate probability for each gRNA to induce effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	211 p_genes = [sum(p_gRNAs[i:i+g-1]) for i in 1:g:n_gRNA_total] # obtain probability of single gene knockout by summing up probability of all corresponding gRNAs to induce effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	212
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	213 # Apply BioCCP functions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	214 E_Nₓ₁ = expectation_minsamplesize(x; p=p_genes, r=r, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	215 sd_Nₓ₁ = std_minsamplesize(x; p=p_genes, r=r, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	216
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	217 return E_Nₓ₁, sd_Nₓ₁
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	218 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	219
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	220
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	221 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	222 simulate_Nₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	223 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	224 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	225 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	226 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	227 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	228 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	229 iter=500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	230
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	231 Computes the expected value and the standard deviation of the minimal plant library size for full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	232 in a multiplex CRISPR/Cas experiment (E[Nx,2] and σ[Nx,2]) using simulation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	233
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	234 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	235 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	236 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	237 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	238 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	239 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	240 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	241 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	242 iter: number of CRISPR/Cas experiments that are simulated to obtain E[Nₓ₂] and σ[Nₓ₂]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	243
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	244 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	245 E_Nₓ₂ : expected value of the plant library size for full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	246 sd_Nₓ₂ : standard deviation on the plant library size for full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	247 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	248 function simulate_Nₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	249 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	250 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	251 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	252 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	253 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	254 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	255 iter = 500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	256
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	257 @assert x * g == n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	258 Nₓ₂_vec = [] #stores number of plants to reach full coverage of all pairwise combinations of gene knockouts for each simulated experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	259
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	260 for i in 1:iter
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	261 X_interactions_count = zeros(x, x) # Initialize matrix to count pairwise interactions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	262 Nₓ₂ = 0
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	263 while X_interactions_count != ones(x, x) # check if all pairwise combinations are present
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	264 Nₓ₂ += 1 # count how many plants must be sampled to fill pairwise interaction matrix
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	265
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	266 # sample combinatorial gRNA/Cas9 construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	267 gRNA_indices_construct = findall((rand(Multinomial(r, p_gRNA_freq))) .!= 0)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	268
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	269 # execute mutations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	270 gRNA_indices_mutations = [gRNA for gRNA in gRNA_indices_construct if rand(Binomial(1, p_gRNA_edit[gRNA])) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	271
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	272 # effective gene knockout (loss-of-function) ?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	273 gRNA_indices_KO = [gRNA for gRNA in gRNA_indices_mutations if rand(Binomial(1, ϵ_KO)) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	274
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	275 # which genes are knocked out?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	276 genes_indices_KO = Int.(ceil.(gRNA_indices_KO / g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	277
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	278 # which pairwise combinations are present?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	279 interactions = collect(combinations(genes_indices_KO, 2))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	280
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	281 # Store represented combinations in matrix
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	282 for interaction in interactions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	283 j = interaction[1]; k = interaction[2]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	284 X_interactions_count[j,k] = 1; X_interactions_count[k,j] = 1; X_interactions_count[j,j] = 1; X_interactions_count[k,k] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	285 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	286 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	287
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	288 push!(Nₓ₂_vec, Nₓ₂)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	289 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	290
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	291 # Calculate expected value and standard deviation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	292 E_Nₓ₂ = mean(Nₓ₂_vec)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	293 sd_Nₓ₂ = std(Nₓ₂_vec)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	294
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	295 return E_Nₓ₂, sd_Nₓ₂
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	296 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	297
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	298 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	299 BioCCP_Nₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	300 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	301 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	302 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	303 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	304 p_gRNA_edit, ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	305
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	306 Computes the expected value and the standard deviation of the minimal plant library size for full coverage of all pairwise combinations of gene knockouts in a multiplex CRISPR/Cas experiment (E[Nx,2] and σ[Nx,2]) using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	307
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	308 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	309 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	310 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	311 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	312 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	313 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	314 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	315 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	316
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	317 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	318 E_Nₓ₂: expected value of the plant library size for full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	319 sd_Nₓ₂: standard deviation on the plant library size for full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	320 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	321 function BioCCP_Nₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	322 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	323 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	324 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	325 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	326 p_gRNA_edit, ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	327
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	328 # how many pairwise combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	329 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 2))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	330 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	331
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	332 # calculate probability and activity of gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	333 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	334 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	335 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	336 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	337 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	338 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	339
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	340 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	341 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	342
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	343 # select pairwise gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	344 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	345 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	346 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	347 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	348 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	349 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	350 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	351 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	352 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	353 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	354
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	355 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	356 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^2
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	357
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	358 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	359 p_genes_matrix = zeros(x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	360 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	361 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	362 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	363 p_genes_matrix[gene1, gene2] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	364 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	365 p_genes = collect([p_genes_matrix[i, j] for j in 2:size(p_genes_matrix, 1) for i in 1:j-1])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	366 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	367 combinations_pp = length(collect(combinations(1:r, 2)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	368
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	369 # Apply BioCCP functions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	370 E_Nₓ₂ = expectation_minsamplesize(n_combinations_genes; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	371 sd_Nₓ₂ = std_minsamplesize(n_combinations_genes; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	372
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	373 return E_Nₓ₂, sd_Nₓ₂
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	374 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	375
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	376 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	377 simulate_Nₓ₂_countKOs(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	378 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	379 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	380 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	381 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	382 p_gRNA_edit, ϵ_KO; iter=100000)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	383
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	384 Counts the number of knockouts per plant in the experiment.
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	385
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	386 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	387 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	388 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	389 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	390 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	391 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	392 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	393 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	394 iter: number of plants that are sampled
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	395
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	396 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	397 n_KOs_vec: vector with the number of knockouts for each plant
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	398 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	399 function simulate_Nₓ₂_countKOs(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	400 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	401 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	402 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	403 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	404 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	405 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	406 iter = 100000)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	407
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	408 @assert x * g == n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	409
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	410 n_KOs_vec = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	411
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	412 for j in 1:iter
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	413 # sample combinatorial gRNA/Cas9 construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	414 gRNA_indices_construct = findall((rand(Multinomial(r, p_gRNA_freq))) .!= 0)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	415
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	416 # execute mutations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	417 gRNA_indices_mutations = [gRNA for gRNA in gRNA_indices_construct if rand(Binomial(1, p_gRNA_edit[gRNA])) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	418
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	419 # effective gene knockout (loss-of-function) ?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	420 gRNA_indices_KO = [gRNA for gRNA in gRNA_indices_mutations if rand(Binomial(1, ϵ_KO)) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	421
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	422 # which genes are knocked out?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	423 genes_indices_KO = Int.(ceil.(gRNA_indices_KO / g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	424
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	425 push!(n_KOs_vec, length(unique((genes_indices_KO))))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	426 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	427
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	428 return n_KOs_vec
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	429 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	430
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	431 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	432 simulate_Nₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	433 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	434 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	435 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	436 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	437 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	438 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	439 iter=500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	440
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	441 Computes the expected value and the standard deviation of the minimal plant library size for full coverage of all triple combinations of gene knockouts in
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	442 a multiplex CRISPR/Cas experiment (E[Nx,3] and σ[Nx,3]) using simulation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	443
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	444 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	445 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	446 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	447 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	448 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	449 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	450 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	451 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	452 iter: number of CRISPR/Cas experiments that are simulated to obtain E[Nₓ₃] and σ[Nₓ₃]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	453
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	454 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	455 E_Nₓ₃: expecteded value of the plant library size for full coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	456 sd_Nₓ₃: standard deviation on the plant library size for full coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	457 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	458 function simulate_Nₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	459 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	460 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	461 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	462 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	463 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	464 ϵ_KO;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	465 iter = 500)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	466
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	467 @assert x * g == n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	468
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	469 Nₓ₃_vec = [] # stores number of plants required for each experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	470
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	471 for i in 1:iter
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	472 # println("got till here")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	473 X_interactions_count = zeros(x, x, x) # Initialize matrix to count triple interactions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	474 # println(X_interactions_count)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	475 # println(ones(x, x, x))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	476 Nₓ₃ = 0
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	477
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	478 while X_interactions_count != ones(x, x, x) # check if all triple combinations are present
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	479 Nₓ₃ += 1 # count how many plants must be sampled to fill triple interaction matrix
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	480
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	481 # sample combinatorial gRNA/Cas9 construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	482 gRNA_indices_construct = findall((rand(Multinomial(r, p_gRNA_freq))) .!= 0)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	483
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	484 # execute mutations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	485 gRNA_indices_mutations = [gRNA for gRNA in gRNA_indices_construct if rand(Binomial(1, p_gRNA_edit[gRNA])) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	486
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	487 # effective gene knockout (loss-of-function) ?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	488 gRNA_indices_KO = [gRNA for gRNA in gRNA_indices_mutations if rand(Binomial(1, ϵ_KO)) == 1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	489
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	490 # which genes are knocked out?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	491 genes_indices_KO = Int.(ceil.(gRNA_indices_KO / g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	492
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	493 # which triple combinations are present?
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	494 interactions = collect(combinations(genes_indices_KO, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	495
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	496 # Store represented triple combinations in 3D-matrix
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	497 for interaction in interactions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	498 j = interaction[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	499 k = interaction[2]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	500 l = interaction[3]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	501 X_interactions_count[j,k,l] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	502 X_interactions_count[k,j,l] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	503 X_interactions_count[l,j,k] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	504 X_interactions_count[l,k,j] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	505 X_interactions_count[j,l,k] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	506 X_interactions_count[k,l,j] = 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	507
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	508 X_interactions_count[:,l,l] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	509 X_interactions_count[:,k,k] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	510 X_interactions_count[:,j,j] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	511 X_interactions_count[l,:,l] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	512 X_interactions_count[k,:,k] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	513 X_interactions_count[j,:,j] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	514
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	515 X_interactions_count[j,j,:] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	516 X_interactions_count[k,k,:] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	517 X_interactions_count[l,l,:] .= 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	518 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	519 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	520 push!(Nₓ₃_vec, Nₓ₃)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	521 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	522
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	523 # calculate expected value and standard deviation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	524 E_Nₓ₃ = mean(Nₓ₃_vec); sd_Nₓ₃ = std(Nₓ₃_vec)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	525
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	526 return E_Nₓ₃, sd_Nₓ₃
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	527 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	528
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	529
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	530 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	531 BioCCP_Nₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	532 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	533 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	534 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	535 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	536 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	537 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	538
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	539 Computes the expected value and the standard deviation of the minimal plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	540 for full coverage of all triple combinations of gene knockouts in a multiplex CRISPR/Cas experiment (E[Nx,3] and σ[Nx,3]) using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	541
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	542 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	543 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	544 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	545 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	546 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	547 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	548 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	549 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	550
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	551 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	552 E_Nₓ₃: expecteded value of the plant library size for full coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	553 sd_Nₓ₃: standard deviation on the plant library size for full coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	554 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	555 function BioCCP_Nₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	556 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	557 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	558 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	559 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	560 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	561 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	562
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	563 # how many triple combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	564 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	565 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	566
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	567 # calculate probability and activity of triple gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	568 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	569 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	570 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	571 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]] * p_gRNA_freq[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	572 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]] * p_gRNA_edit[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	573 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	574
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	575 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	576 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	577
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	578 # select triple gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	579 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	580 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	581 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	582 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	583 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g) && ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][3]/g) && ceil(ind_combinations_gRNA[i][3]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	584 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	585 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	586 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	587 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	588 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	589
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	590 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	591 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^3
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	592
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	593 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	594 p_genes_matrix = zeros(x, x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	595 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	596 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	597 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	598 gene3 = Int(ceil(ind_combinations_gRNA_interest[i][3]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	599 p_genes_matrix[gene1, gene2, gene3] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	600 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	601
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	602 combinations_genes = collect(combinations(1:x, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	603 p_genes = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	604 for combination in combinations_genes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	605 push!(p_genes, p_genes_matrix[combination[1], combination[2], combination[3]])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	606 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	607
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	608 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	609 combinations_pp = length(collect(combinations(1:r, 3)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	610
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	611 # apply BioCCP functions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	612 E_Nₓ₃ = expectation_minsamplesize(n_combinations_genes; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	613 sd_Nₓ₃ = std_minsamplesize(n_combinations_genes; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	614
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	615 return E_Nₓ₃, sd_Nₓ₃
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	616 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	617
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	618 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	619 BioCCP_Pₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	620 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	621 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	622 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	623 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	624 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	625 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	626 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	627
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	628 Computes the probability of full coverage of all single gene knockouts (Px,1) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	629
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	630 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	631 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	632 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	633 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	634 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	635 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	636 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	637 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	638 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	639
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	640 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	641 Pₓ₁: probability of full coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	642
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	643 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	644 function BioCCP_Pₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	645 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	646 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	647 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	648 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	649 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	650 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	651 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	652
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	653 # prepare input
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	654 p_gRNAs = p_gRNA_freq .* p_gRNA_edit * ϵ_KO
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	655 p_genes = [sum(p_gRNAs[i:i+g-1]) for i in 1:g:n_gRNA_total]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	656
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	657 # apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	658 Pₓ₁ = success_probability(x, N; p=p_genes, r=r, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	659
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	660 return Pₓ₁
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	661 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	662
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	663 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	664 BioCCP_γₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	665 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	666 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	667 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	668 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	669 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	670 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	671 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	672
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	673 Computes the expected coverage of all single gene knockouts (Px,1) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	674
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	675 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	676 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	677 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	678 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	679 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	680 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	681 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	682 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	683 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	684
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	685 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	686 γₓ₁: expected coverage of all single gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	687 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	688 function BioCCP_γₓ₁(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	689 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	690 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	691 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	692 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	693 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	694 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	695 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	696
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	697 p_gRNAs = p_gRNA_freq .* p_gRNA_edit * ϵ_KO
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	698 p_genes = [sum(p_gRNAs[i:i+g-1]) for i in 1:g:n_gRNA_total]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	699
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	700 # Apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	701 γₓ₁ = expectation_fraction_collected(x, N; p=p_genes, r=r, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	702
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	703 return γₓ₁
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	704 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	705
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	706
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	707 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	708 BioCCP_Pₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	709 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	710 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	711 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	712 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	713 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	714 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	715 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	716
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	717 Computes the probability of full coverage of all pairwise combinations of gene knockouts (Px,2) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	718
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	719 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	720 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	721 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	722 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	723 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	724 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	725 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	726 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	727 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	728
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	729 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	730 Pₓ₂: probability of full coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	731 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	732 function BioCCP_Pₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	733 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	734 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	735 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	736 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	737 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	738 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	739 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	740
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	741 # how many pairwise combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	742 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 2))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	743 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	744
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	745 # calculate probability and activity of gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	746 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	747 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	748 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	749 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	750 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	751 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	752
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	753 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	754 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	755
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	756 # select pairwise gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	757 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	758 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	759 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	760 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	761 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	762 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	763 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	764 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	765 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	766 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	767
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	768 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	769 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^2
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	770
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	771 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	772 p_genes_matrix = zeros(x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	773 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	774 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	775 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	776 p_genes_matrix[gene1, gene2] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	777 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	778
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	779 p_genes = collect([p_genes_matrix[i, j] for j in 2:size(p_genes_matrix, 1) for i in 1:j-1])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	780 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	781 combinations_pp = length(collect(combinations(1:r, 2)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	782
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	783 # Apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	784 Pₓ₂ = success_probability(n_combinations_genes, N; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	785
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	786 return Pₓ₂
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	787 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	788
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	789 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	790 BioCCP_γₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	791 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	792 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	793 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	794 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	795 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	796 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	797 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	798
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	799 Computes the expected coverage of all pairwise combinations of gene knockouts (γx,2) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	800
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	801 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	802 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	803 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	804 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	805 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	806 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	807 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	808 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	809 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	810
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	811 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	812 γₓ₂: expected coverage of all pairwise combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	813 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	814 function BioCCP_γₓ₂(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	815 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	816 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	817 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	818 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	819 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	820 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	821 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	822
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	823 # how many pairwise combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	824 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 2))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	825 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	826
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	827 # calculate probability and activity of gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	828 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	829 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	830 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	831 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	832 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	833 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	834
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	835 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	836 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	837
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	838 # select pairwise gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	839 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	840 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	841 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	842 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	843 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	844 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	845 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	846 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	847 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	848 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	849
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	850 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	851 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^2
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	852
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	853 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	854 p_genes_matrix = zeros(x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	855 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	856 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	857 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	858 p_genes_matrix[gene1, gene2] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	859 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	860
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	861 p_genes = collect([p_genes_matrix[i, j] for j in 2:size(p_genes_matrix, 1) for i in 1:j-1])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	862 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	863 combinations_pp = length(collect(combinations(1:r, 2)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	864
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	865 # Apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	866 γₓ₂ = expectation_fraction_collected(n_combinations_genes, N; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	867
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	868 return γₓ₂
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	869 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	870
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	871
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	872 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	873 BioCCP_γₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	874 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	875 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	876 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	877 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	878 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	879 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	880 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	881
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	882 Computes the expected coverage of all triple combinations of gene knockouts (γx,3) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	883
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	884 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	885 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	886 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	887 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	888 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	889 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	890 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	891 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	892 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	893
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	894 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	895 γₓ₃: expected coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	896 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	897 function BioCCP_γₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	898 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	899 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	900 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	901 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	902 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	903 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	904 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	905
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	906 # how many triple combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	907 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	908 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	909
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	910 # calculate probability and activity of triple gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	911 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	912 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	913 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	914 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]] * p_gRNA_freq[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	915 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]] * p_gRNA_edit[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	916 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	917
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	918 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	919 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	920
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	921 # select triple gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	922 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	923 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	924 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	925 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	926 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g) && ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][3]/g) && ceil(ind_combinations_gRNA[i][3]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	927 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	928 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	929 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	930 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	931 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	932
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	933 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	934 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^3
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	935
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	936 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	937 p_genes_matrix = zeros(x, x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	938 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	939 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	940 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	941 gene3 = Int(ceil(ind_combinations_gRNA_interest[i][3]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	942 p_genes_matrix[gene1, gene2, gene3] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	943 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	944
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	945 combinations_genes = collect(combinations(1:x, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	946 p_genes = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	947 for combination in combinations_genes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	948 push!(p_genes, p_genes_matrix[combination[1], combination[2], combination[3]])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	949 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	950
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	951 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	952 combinations_pp = length(collect(combinations(1:r, 3)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	953
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	954 # Apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	955 γₓ₃ = expectation_fraction_collected(n_combinations_genes, N; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	956
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	957 return γₓ₃
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	958 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	959
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	960 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	961 BioCCP_Pₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	962 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	963 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	964 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	965 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	966 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	967 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	968 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	969
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	970 Computes the probability of full coverage of all triple combinations of gene knockouts (Px,3) for an experiment with given plant library size using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	971
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	972 *INPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	973 x: number of target genes in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	974 N: plant library size
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	975 g: number of gRNAs designed per target gene
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	976 r: number of gRNA sequences per combinatorial gRNA/Cas construct
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	977 n_gRNA_total: total number of gRNAs in the experiment
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	978 p_gRNA_freq: vector with relative frequencies for all gRNAs in the construct library (normalized!)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	979 p_gRNA_edit: vector with genome editing efficiencies for all gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	980 ϵ_KO: global knockout efficiency; fraction of mutations leading to effective gene knockout
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	981
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	982 *OUTPUT*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	983 Pₓ₃: probability of full coverage of all triple combinations of gene knockouts
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	984 """
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	985 function BioCCP_Pₓ₃(x,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	986 N,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	987 g,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	988 r,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	989 n_gRNA_total,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	990 p_gRNA_freq,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	991 p_gRNA_edit,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	992 ϵ_KO)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	993
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	994 # how many triple combinations of gRNAs
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	995 ind_combinations_gRNA = collect(combinations(1:n_gRNA_total, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	996 n_combinations_gRNA = length(ind_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	997
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	998 # calculate probability and activity of triple gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	999 p_combinations_gRNA_library = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1000 p_combinations_gRNA_act = zeros(n_combinations_gRNA)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1001 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1002 p_combinations_gRNA_library[i] = p_gRNA_freq[ind_combinations_gRNA[i][1]] * p_gRNA_freq[ind_combinations_gRNA[i][2]] * p_gRNA_freq[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1003 p_combinations_gRNA_act[i] = p_gRNA_edit[ind_combinations_gRNA[i][1]] * p_gRNA_edit[ind_combinations_gRNA[i][2]] * p_gRNA_edit[ind_combinations_gRNA[i][3]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1004 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1005
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1006 # normalize probability gRNA combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1007 p_combinations_gRNA_library /= sum(p_combinations_gRNA_library)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1008
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1009 # select triple gRNA combinations of which each component codes for different gene (goal is to study combinations of knockouts in different genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1010 p_combinations_gRNA_library_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1011 p_combinations_gRNA_act_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1012 ind_combinations_gRNA_interest = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1013 for i in 1:n_combinations_gRNA
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1014 if ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][2]/g) && ceil(ind_combinations_gRNA[i][1]/g) != ceil(ind_combinations_gRNA[i][3]/g) && ceil(ind_combinations_gRNA[i][3]/g) != ceil(ind_combinations_gRNA[i][2]/g)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1015 push!(p_combinations_gRNA_library_interest, p_combinations_gRNA_library[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1016 push!(p_combinations_gRNA_act_interest, p_combinations_gRNA_act[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1017 push!(ind_combinations_gRNA_interest, ind_combinations_gRNA[i])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1018 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1019 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1020
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1021 n_combinations_gRNA_interest = length(p_combinations_gRNA_library_interest)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1022 p_combinations_gRNA = p_combinations_gRNA_library_interest .* p_combinations_gRNA_act_interest * ϵ_KO^3
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1023
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1024 # sum up probabilities or gRNA combinations for corresponding gene knockout combinations
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1025 p_genes_matrix = zeros(x, x, x)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1026 for i in 1:n_combinations_gRNA_interest
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1027 gene1 = Int(ceil(ind_combinations_gRNA_interest[i][1]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1028 gene2 = Int(ceil(ind_combinations_gRNA_interest[i][2]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1029 gene3 = Int(ceil(ind_combinations_gRNA_interest[i][3]/g))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1030 p_genes_matrix[gene1, gene2, gene3] += p_combinations_gRNA[i]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1031 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1032
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1033 combinations_genes = collect(combinations(1:x, 3))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1034 p_genes = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1035 for combination in combinations_genes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1036 push!(p_genes, p_genes_matrix[combination[1], combination[2], combination[3]])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1037 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1038
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1039 n_combinations_genes = length(p_genes)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1040 combinations_pp = length(collect(combinations(1:r, 3)))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1041
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1042 # Apply BioCCP function
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1043 Pₓ₃ = success_probability(n_combinations_genes, N; p=p_genes, r=combinations_pp, normalize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1044
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1045 return Pₓ₃
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1046 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1047
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1048

Mercurial > repos > padge > mcdoe

annotate MultiplexCrisprDOE.jl @ 1:4a5c94d1d8bb draft