Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-subset.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # Load optparse we need to check inputs
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4
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5 suppressPackageStartupMessages(require(optparse))
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6
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7 # Load common functions
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8
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9 suppressPackageStartupMessages(require(workflowscriptscommon))
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10
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11 # parse options
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12
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13 option_list = list(
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14 make_option(
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15 c("--signac-object"),
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16 action = "store",
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17 default = NA,
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18 type = 'character',
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19 help = ""
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20 ),
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21 make_option(
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22 c("--peak-region-fragments-min"),
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23 action = "store",
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24 default = NA,
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25 type = 'character',
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26 help = "."
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27 ),
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28 make_option(
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29 c("--peak-region-fragments-max"),
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30 action = "store",
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31 default = NA,
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32 type = 'character',
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33 help = "."
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34 ),
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35 make_option(
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36 c("--pct-reads-in-peaks"),
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37 action = "store",
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38 default = NA,
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39 type = 'character',
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40 help = "."
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41 ),
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42 make_option(
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43 c("--blacklist-ratio"),
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44 action = "store",
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45 default = NA,
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46 type = 'character',
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47 help = "."
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48 ),
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49 make_option(
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50 c("--nucleosome-signal"),
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51 action = "store",
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52 default = NA,
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53 type = 'character',
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54 help = "."
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55 ),
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56 make_option(
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57 c("--tss-enrichment"),
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58 action = "store",
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59 default = NA,
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60 type = 'character',
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61 help = "."
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62 ),
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63 make_option(
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64 c("--output-object-file"),
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65 action = "store",
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66 default = NA,
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67 type = 'character',
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68 help = "File name in which to store serialized R matrix object."
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69 )
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70 )
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71
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72 opt <- wsc_parse_args(option_list)
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73
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74 suppressPackageStartupMessages(require(Signac))
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75
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76 # extract gene annotations from EnsDb
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77 signac_object <- readRDS(file = opt$signac_object)
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78
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79
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80 ## transform input parameters to numeric
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81 peak_region_fragments_min <- as.numeric(opt$peak_region_fragments_min)
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82 peak_region_fragments_max <- as.numeric(opt$peak_region_fragments_max)
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83 pct_reads_in_peaks_var <- as.numeric(opt$pct_reads_in_peaks)
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84 blacklist_ratio_var <- as.numeric(opt$blacklist_ratio)
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85 nucleosome_signal_var <- as.numeric(opt$nucleosome_signal)
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86 tss_enrichment_var <- as.numeric(opt$tss_enrichment)
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87
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88 print("Signac object before filtering:")
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89
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90 signac_object
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91
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92 signac_object <- subset(signac_object, peak_region_fragments > peak_region_fragments_min)
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93 signac_object <- subset(signac_object, peak_region_fragments < peak_region_fragments_max)
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94 signac_object <- subset(signac_object, pct_reads_in_peaks > pct_reads_in_peaks_var)
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95 signac_object <- subset(signac_object, blacklist_ratio < blacklist_ratio_var)
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96 signac_object <- subset(signac_object, nucleosome_signal < nucleosome_signal_var)
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97 signac_object <- subset(signac_object, TSS.enrichment > tss_enrichment_var)
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98
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99 print("Signac object after filtering:")
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100
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101 signac_object
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102
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103 # Output to a serialized R object
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104 saveRDS(signac_object, file = opt$output_object_file)