ms2snoop: MS2snoop.R annotate

author	workflow4metabolomics
date	Mon, 25 Apr 2022 08:23:54 +0000
parents
children	df2672c37732

rev	line source
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	2 #' read and process mspurity W4M files
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	3 #' create a summary of fragment for each precursor and a graphics of peseudo
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	4 #' spectra + correlation on which checking of fragment is based on
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	5 #' V3 try to identify and process multiple files for 1 precursor which may
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	6 #' occur if different collision energy are used
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	7 #' V4 elimination of correlation = NA. Correlation is done with precursor, if
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	8 #' precursor is not present correlation with most intense peak
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	9 #' author: Jean-Francois Martin
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	10 #' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	11 #' tested against data from other labs.
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	12 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	13 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	14 #' @import optparse
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	15 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	16 NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	17
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	18
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	19 assign("DEFAULT_PRECURSOR_PATH", "peaklist_precursors.tsv")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	20 assign("DEFAULT_FRAGMENTS_PATH", "peaklist_fragments.tsv")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	21 assign("DEFAULT_COMPOUNDS_PATH", "compounds_pos.txt")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	22 assign("DEFAULT_OUTPUT_PATH", "compound_fragments_result.txt")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	23 assign("DEFAULT_TOLMZ", 0.01)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	24 assign("DEFAULT_TOLRT", 20)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	25 assign("DEFAULT_MZDECIMAL", 0)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	26 assign("DEFAULT_R_THRESHOLD", 0.85)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	27 assign("DEFAULT_MINNUMBERSCAN", 8)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	28 assign("DEFAULT_SEUIL_RA", 0.5)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	29 lockBinding("DEFAULT_PRECURSOR_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	30 lockBinding("DEFAULT_FRAGMENTS_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	31 lockBinding("DEFAULT_COMPOUNDS_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	32 lockBinding("DEFAULT_OUTPUT_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	33 lockBinding("DEFAULT_TOLMZ", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	34 lockBinding("DEFAULT_TOLRT", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	35 lockBinding("DEFAULT_MZDECIMAL", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	36 lockBinding("DEFAULT_R_THRESHOLD", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	37 lockBinding("DEFAULT_MINNUMBERSCAN", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	38 lockBinding("DEFAULT_SEUIL_RA", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	39
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	40 assign("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", 0.85)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	41 assign("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", 0.1)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	42 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", 0.01)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	43 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", 60)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	44 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	45 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	46 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	47 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	48
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	49
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	50 debug <- FALSE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	51
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	52
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	53 ########################################################################
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	54
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	55 #' @title plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	56 #' @param x
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	57 #' @param r_threshold
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	58 #' @param fid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	59 #' @param sum_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	60 #' @param vmz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	61 #' @param cor_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	62 #' @param refcol
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	63 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	64 #' @description plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	65 #' function to compute sum of intensities among scans for all
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	66 #' m/z kept (cor > r_threshold & minimum number of scans)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	67 #' and plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	68 #' x dataframe scan X fragments with scans number in the 1st column and
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	69 #' ions in next with intensities
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	70 #' fid file id when several a precursor has been detected in several files
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	71 plot_pseudo_spectra <- function(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	72 x,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	73 r_threshold,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	74 fid,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	75 sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	76 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	77 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	78 refcol,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	79 c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	80 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	81 ## du fait de la difference de nombre de colonne entre la dataframe qui
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	82 ## inclue les scans en 1ere col, mzRef se decale de 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	83 refcol <- refcol - 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	84 ## compute relative intensities max=100%
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	85 rel_int <- sum_int[-1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	86 rel_int <- rel_int / max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	87
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	88 ## define max value on vertical axis (need to increase in order to plot the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	89 ## label of fragments)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	90 ymax <- max(rel_int) + 0.2 * max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	91
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	92 par(mfrow = c(2, 1))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	93 plot(vmz, rel_int, type = "h", ylim = c(0, ymax), main = c_name)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	94 ## low correl coef. will be display in grey
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	95 cor_low <- which(round(cor_abs_int, 2) < r_threshold)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	96
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	97 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	98
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	99 if (length(cor_low) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	100 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	101 vmz[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	102 rel_int[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	103 lbmzcor[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	104 cex = 0.5,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	105 col = "grey",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	106 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	107 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	108 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	109 if (length(vmz) - length(cor_low) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	110 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	111 vmz[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	112 rel_int[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	113 lbmzcor[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	114 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	115 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	116 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	117 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	118 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	119 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	120 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	121 if (length(vmz) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	122 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	123 vmz[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	124 rel_int[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	125 lbmzcor[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	126 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	127 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	128 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	129 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	130 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	131 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	132 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	133
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	134 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	135 vmz[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	136 rel_int[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	137 lbmzcor[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	138 cex = 0.8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	139 col = 2,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	140 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	141 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	142 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	143
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	144 ## prepare result file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	145 corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	146 cp_res <- data.frame(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	147 rep(c_name, length(vmz)),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	148 rep(fid, length(vmz)),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	149 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	150 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	151 sum_int[-1],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	152 rel_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	153 corValid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	154 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	155
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	156 colnames(cp_res) <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	157 "compoundName",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	158 "fileid",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	159 "fragments_mz",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	160 "CorWithPrecursor",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	161 "AbsoluteIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	162 "relativeIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	163 "corValid"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	164 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	165 return(cp_res)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	166
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	167 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	168
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	169 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	170 #' @title extract_fragments
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	171 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	172 #' @param precursors the precursor list from mspurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	173 #' @param fragments the fragments list from ms purity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	174 #' @param mzref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	175 #' @param rtref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	176 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	177 #' @param r_threshold default = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	178 #' @param seuil_ra default = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	179 #' @param tolmz default = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	180 #' @param tolrt default = DEFAULT_EXTRACT_FRAGMENTS_TOLRT
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	181 #' @returns
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	182 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	183 #' @description
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	184 #' function for extraction of fragments corresponding to precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	185 #' detected by MSPurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	186 extract_fragments <- function( ## nolint cyclocomp_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	187 precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	188 fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	189 mzref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	190 rtref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	191 c_name,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	192 min_number_scan,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	193 mzdecimal,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	194 r_threshold=DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	195 seuil_ra=DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	196 tolmz=DEFAULT_EXTRACT_FRAGMENTS_TOLMZ,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	197 tolrt=DEFAULT_EXTRACT_FRAGMENTS_TOLRT
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	198 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	199 ## filter precursor in the precursors file based on mz and rt in the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	200 ## compound list
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	201 cat("processing ", c_name, "\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	202 selected_precursors <- which(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	203 (abs(precursors$precurMtchMZ - mzref) <= tolmz)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	204 & (abs(precursors$precurMtchRT - rtref) <= tolrt)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	205 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	206
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	207 ## check if there is the precursor in the file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	208 if (length(selected_precursors) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	209
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	210 sprecini <- precursors[selected_precursors, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	211
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	212 ## check if fragments corresponding to precursor are found in several
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	213 ## files (collision energy)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	214 ## this lead to a processing for each fileid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	215 mf <- levels(as.factor(sprecini$fileid))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	216 if (length(mf) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	217 cat(" several files detected for this compounds :\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	218 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	219
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	220 for (f in seq_along(mf)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	221
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	222 sprec <- sprecini[sprecini$fileid == mf[f], ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	223
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	224 ## selection of fragment in the fragments file with the grpid common in
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	225 ## both fragments and precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	226 selfrgt <- levels(as.factor(sprec$grpid))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	227 sfrgt <- fragments[
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	228 fragments$grpid %in% selfrgt
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	229 & fragments$fileid == mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	230 ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	231
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	232 ## filter fragments on relative intensity seuil_ra = user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	233 ## parameter (MSpurity flags could be used here)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	234 sfrgtfil <- sfrgt[sfrgt$ra > seuil_ra, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	235
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	236 mznominal <- round(x = sfrgtfil$mz, mzdecimal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	237 sfrgtfil <- data.frame(sfrgtfil, mznominal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	238
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	239 ## creation of cross table row=scan col=mz X=ra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	240 vmz <- levels(as.factor(sfrgtfil$mznominal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	241
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	242 cat(" fragments :", vmz)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	243
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	244 ## mz of precursor in data precursor to check correlation with
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	245 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	246
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	247 for (m in seq_along(vmz)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	248
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	249 ## absolute intensity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	250 cln <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	251 which(colnames(sfrgtfil) == "acquisitionNum"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	252 which(colnames(sfrgtfil) == "i")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	253 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	254 int_mz <- sfrgtfil[sfrgtfil$mznominal == vmz[m], cln]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	255 colnames(int_mz)[2] <- paste0("mz", vmz[m])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	256
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	257 ## average intensities of mass in duplicate scans
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	258 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	259 int_mz <- comp_scans[, -1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	260
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	261 if (m == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	262 ds_abs_int <- int_mz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	263 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	264 ds_abs_int <- merge(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	265 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	266 y = int_mz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	267 by.x = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	268 by.y = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	269 all.x = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	270 all.y = TRUE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	271 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	272 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	273 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	274 if (debug) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	275 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	276 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	277 file = paste0(c_name, "ds_abs_int.txt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	278 row.names = FALSE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	279 sep = "\t"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	280 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	281 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	282
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	283 ## elimination of mz with less than min_number_scan scans (user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	284 ## parameter)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	285 xmz <- rep(NA, ncol(ds_abs_int) - 1)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	286 sum_int <- rep(NA, ncol(ds_abs_int))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	287 nbxmz <- 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	288 nb_scan_check <- min(nrow(ds_abs_int), min_number_scan)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	289
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	290 for (j in 2:ncol(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	291 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	292 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	293 nbxmz <- nbxmz + 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	294 xmz[nbxmz] <- j
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	295 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	296 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	297
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	298 xmz <- xmz[-which(is.na(xmz))]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	299 if (length(xmz) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	300 ds_abs_int <- ds_abs_int[, -c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	301 sum_int <- sum_int[-c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	302 ## liste des mz keeped decale de 1 avec ds_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	303 vmz <- as.numeric(vmz[-c(xmz - 1)])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	304 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	305
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	306 ## reference ion for correlation computing = precursor OR maximum
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	307 ## intensity ion in precursor is not present
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	308 refcol <- which(colnames(ds_abs_int) == mz_prec)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	309 if (length(refcol) == 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	310 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	311 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	312 pdf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	313 file = sprintf("%s_processing_file%s.pdf", c_name, mf[f]),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	314 width = 8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	315 height = 11
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	316 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	317 par(mfrow = c(3, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	318
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	319 ## Pearson correlations between absolute intensities computing
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	320 cor_abs_int <- rep(NA, length(vmz))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	321
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	322 if (length(refcol) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	323 for (i in 2:length(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	324 cor_abs_int[i - 1] <- cor(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	325 x = ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	326 y = ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	327 use = "pairwise.complete.obs",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	328 method = "pearson"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	329 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	330 plot(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	331 ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	332 ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	333 xlab = colnames(ds_abs_int)[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	334 ylab = colnames(ds_abs_int)[i],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	335 main = sprintf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	336 "%s corr coeff r=%s", c_name, round(cor_abs_int[i - 1], 2)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	337 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	338 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	339 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	340 ## plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	341 res_comp_by_file <- plot_pseudo_spectra(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	342 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	343 r_threshold = r_threshold,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	344 fid = mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	345 sum_int = sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	346 vmz = vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	347 cor_abs_int = cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	348 refcol = refcol,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	349 c_name = c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	350 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	351 if (f == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	352 res_comp <- res_comp_by_file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	353 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	354 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	355 res_comp_by_file <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	356 cat(" non detected in fragments file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	357 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	358 if (!is.null(res_comp_by_file)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	359 res_comp <- rbind(res_comp, res_comp_by_file)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	360 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	361 cat("\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	362 dev.off()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	363 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	364 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	365 res_comp <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	366 cat(" non detected in precursor file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	367 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	368 return(res_comp)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	369 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	370
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	371
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	372 create_parser <- function() {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	373 parser <- optparse::OptionParser()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	374 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	375 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	376 c("-v", "--verbose"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	377 action = "store_true",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	378 default = FALSE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	379 help = "Print extra output [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	380 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	381 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	382 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	383 c("-o", "--output"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	384 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	385 default = DEFAULT_OUTPUT_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	386 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	387 help = "Path to the output file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	388 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	389 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	390 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	391 c("-p", "--precursors"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	392 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	393 default = DEFAULT_PRECURSOR_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	394 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	395 help = "Path to the precursors file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	396 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	397 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	398 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	399 c("-f", "--fragments"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	400 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	401 default = DEFAULT_FRAGMENTS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	402 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	403 help = "Path to the fragments file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	404 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	405 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	406 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	407 c("-c", "--compounds"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	408 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	409 default = DEFAULT_COMPOUNDS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	410 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	411 help = "Path to the compounds file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	412 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	413 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	414 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	415 c("--tolmz"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	416 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	417 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	418 default = DEFAULT_TOLMZ,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	419 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	420 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	421 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	422 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	423 c("--tolrt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	424 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	425 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	426 default = DEFAULT_TOLRT,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	427 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	428 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	429 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	430 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	431 c("--seuil_ra"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	432 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	433 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	434 help = "relative intensity threshold",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	435 default = DEFAULT_SEUIL_RA,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	436 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	437 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	438 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	439 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	440 c("--mzdecimal"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	441 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	442 default = DEFAULT_MZDECIMAL,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	443 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	444 help = "nb decimal for mz",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	445 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	446 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	447 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	448 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	449 c("--r_threshold"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	450 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	451 default = DEFAULT_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	452 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	453 help = paste0(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	454 "r pearson correlation threshold between precursor and fragment ",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	455 "absolute intensity"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	456 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	457 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	458 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	459 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	460 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	461 c("--min_number_scan"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	462 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	463 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	464 default = DEFAULT_MINNUMBERSCAN,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	465 help = paste0(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	466 "fragments are kept if there are found in a minimum number ",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	467 "of scans"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	468 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	469 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	470 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	471 return(parser)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	472 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	473
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	474 main <- function(args) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	475 ## FOLDER AND FILES
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	476 ## MSpurity precursors file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	477 precursors <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	478 file = args$precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	479 header = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	480 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	481 quote = "\""
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	482 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	483 ## MSpurity fragments file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	484 fragments <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	485 file = args$fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	486 header = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	487 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	488 quote = "\""
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	489 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	490 ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	491 compounds <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	492 file = args$compounds,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	493 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	494 quote = "\"",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	495 header = TRUE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	496 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	497 ## PARAMETERS
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	498 ## tolerance for mz(dalton) rt(seconds) to match the standard in the compounds
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	499 ## list with the precursor MSpurity file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	500 tolmz <- args$tolmz

0

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1 #'

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2 #' read and process mspurity W4M files

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3 #' create a summary of fragment for each precursor and a graphics of peseudo

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4 #' spectra + correlation on which checking of fragment is based on

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5 #' V3 try to identify and process multiple files for 1 precursor which may

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6 #' occur if different collision energy are used

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7 #' V4 elimination of correlation = NA. Correlation is done with precursor, if

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8 #' precursor is not present correlation with most intense peak

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9 #' author: Jean-Francois Martin

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10 #' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and

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11 #' tested against data from other labs.

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12 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr

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13 #'

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14 #' @import optparse

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15 #'

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16 NULL

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17

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18

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19 assign("DEFAULT_PRECURSOR_PATH", "peaklist_precursors.tsv")

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20 assign("DEFAULT_FRAGMENTS_PATH", "peaklist_fragments.tsv")

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21 assign("DEFAULT_COMPOUNDS_PATH", "compounds_pos.txt")

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22 assign("DEFAULT_OUTPUT_PATH", "compound_fragments_result.txt")

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23 assign("DEFAULT_TOLMZ", 0.01)

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24 assign("DEFAULT_TOLRT", 20)

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25 assign("DEFAULT_MZDECIMAL", 0)

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26 assign("DEFAULT_R_THRESHOLD", 0.85)

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27 assign("DEFAULT_MINNUMBERSCAN", 8)

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28 assign("DEFAULT_SEUIL_RA", 0.5)

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29 lockBinding("DEFAULT_PRECURSOR_PATH", globalenv())

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30 lockBinding("DEFAULT_FRAGMENTS_PATH", globalenv())

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31 lockBinding("DEFAULT_COMPOUNDS_PATH", globalenv())

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32 lockBinding("DEFAULT_OUTPUT_PATH", globalenv())

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33 lockBinding("DEFAULT_TOLMZ", globalenv())

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34 lockBinding("DEFAULT_TOLRT", globalenv())

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35 lockBinding("DEFAULT_MZDECIMAL", globalenv())

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36 lockBinding("DEFAULT_R_THRESHOLD", globalenv())

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37 lockBinding("DEFAULT_MINNUMBERSCAN", globalenv())

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38 lockBinding("DEFAULT_SEUIL_RA", globalenv())

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39

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40 assign("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", 0.85)

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41 assign("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", 0.1)

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42 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", 0.01)

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43 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", 60)

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44 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", globalenv())

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45 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", globalenv())

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46 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", globalenv())

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47 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", globalenv())

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48

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49

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50 debug <- FALSE

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51

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52

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53 ########################################################################

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54

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55 #' @title plot_pseudo_spectra

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56 #' @param x

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57 #' @param r_threshold

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58 #' @param fid

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59 #' @param sum_int

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60 #' @param vmz

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61 #' @param cor_abs_int

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62 #' @param refcol

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63 #' @param c_name

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64 #' @description plot_pseudo_spectra

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65 #' function to compute sum of intensities among scans for all

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66 #' m/z kept (cor > r_threshold & minimum number of scans)

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67 #' and plot pseudo spectra

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68 #' x dataframe scan X fragments with scans number in the 1st column and

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69 #' ions in next with intensities

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70 #' fid file id when several a precursor has been detected in several files

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71 plot_pseudo_spectra <- function(

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72 x,

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73 r_threshold,

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74 fid,

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75 sum_int,

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76 vmz,

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77 cor_abs_int,

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78 refcol,

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79 c_name

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80 ) {

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81 ## du fait de la difference de nombre de colonne entre la dataframe qui

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82 ## inclue les scans en 1ere col, mzRef se decale de 1

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83 refcol <- refcol - 1

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84 ## compute relative intensities max=100%

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85 rel_int <- sum_int[-1]

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86 rel_int <- rel_int / max(rel_int)

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87

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88 ## define max value on vertical axis (need to increase in order to plot the

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89 ## label of fragments)

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90 ymax <- max(rel_int) + 0.2 * max(rel_int)

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91

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92 par(mfrow = c(2, 1))

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93 plot(vmz, rel_int, type = "h", ylim = c(0, ymax), main = c_name)

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94 ## low correl coef. will be display in grey

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95 cor_low <- which(round(cor_abs_int, 2) < r_threshold)

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96

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97 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))

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98

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99 if (length(cor_low) > 0) {

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100 text(

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101 vmz[cor_low],

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102 rel_int[cor_low],

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103 lbmzcor[cor_low],

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104 cex = 0.5,

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105 col = "grey",

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106 srt = 90,

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107 adj = 0

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108 )

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109 if (length(vmz) - length(cor_low) > 1) {

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110 text(

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111 vmz[-c(refcol, cor_low)],

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112 rel_int[-c(refcol, cor_low)],

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113 lbmzcor[-c(refcol, cor_low)],

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114 cex = 0.6,

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115 col = 1,

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116 srt = 90,

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117 adj = 0

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118 )

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119 }

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120 } else {

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121 if (length(vmz) > 1) {

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122 text(

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123 vmz[-c(refcol)],

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124 rel_int[-c(refcol)],

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125 lbmzcor[-c(refcol)],

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126 cex = 0.6,

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127 col = 1,

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128 srt = 90,

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129 adj = 0

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130 )

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131 }

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132 }

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133

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134 text(

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135 vmz[refcol],

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136 rel_int[refcol],

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137 lbmzcor[refcol],

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138 cex = 0.8,

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139 col = 2,

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140 srt = 90,

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141 adj = 0

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142 )

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143

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144 ## prepare result file

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145 corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter

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146 cp_res <- data.frame(

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147 rep(c_name, length(vmz)),

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148 rep(fid, length(vmz)),

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149 vmz,

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150 cor_abs_int,

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151 sum_int[-1],

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152 rel_int,

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153 corValid

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154 )

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155

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156 colnames(cp_res) <- c(

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157 "compoundName",

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158 "fileid",

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159 "fragments_mz",

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160 "CorWithPrecursor",

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161 "AbsoluteIntensity",

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162 "relativeIntensity",

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163 "corValid"

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164 )

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165 return(cp_res)

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166

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167 }

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168

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169 #'

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170 #' @title extract_fragments

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171 #'

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172 #' @param precursors the precursor list from mspurity

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173 #' @param fragments the fragments list from ms purity

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174 #' @param mzref

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175 #' @param rtref

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176 #' @param c_name

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177 #' @param r_threshold default = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD

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178 #' @param seuil_ra default = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA

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179 #' @param tolmz default = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ

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180 #' @param tolrt default = DEFAULT_EXTRACT_FRAGMENTS_TOLRT

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181 #' @returns

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182 #'

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183 #' @description

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184 #' function for extraction of fragments corresponding to precursors

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185 #' detected by MSPurity

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186 extract_fragments <- function( ## nolint cyclocomp_linter

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187 precursors,

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188 fragments,

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189 mzref,

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190 rtref,

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191 c_name,

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192 min_number_scan,

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193 mzdecimal,

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194 r_threshold=DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD,

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195 seuil_ra=DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA,

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196 tolmz=DEFAULT_EXTRACT_FRAGMENTS_TOLMZ,

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197 tolrt=DEFAULT_EXTRACT_FRAGMENTS_TOLRT

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198 ) {

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199 ## filter precursor in the precursors file based on mz and rt in the

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200 ## compound list

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201 cat("processing ", c_name, "\n")

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202 selected_precursors <- which(

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203 (abs(precursors$precurMtchMZ - mzref) <= tolmz)

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204 & (abs(precursors$precurMtchRT - rtref) <= tolrt)

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205 )

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206

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207 ## check if there is the precursor in the file

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208 if (length(selected_precursors) > 0) {

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209

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210 sprecini <- precursors[selected_precursors, ]

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211

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212 ## check if fragments corresponding to precursor are found in several

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213 ## files (collision energy)

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214 ## this lead to a processing for each fileid

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215 mf <- levels(as.factor(sprecini$fileid))

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216 if (length(mf) > 1) {

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217 cat(" several files detected for this compounds :\n")

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218 }

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219

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220 for (f in seq_along(mf)) {

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221

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222 sprec <- sprecini[sprecini$fileid == mf[f], ]

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223

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224 ## selection of fragment in the fragments file with the grpid common in

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225 ## both fragments and precursors

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226 selfrgt <- levels(as.factor(sprec$grpid))

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227 sfrgt <- fragments[

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228 fragments$grpid %in% selfrgt

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229 & fragments$fileid == mf[f],

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230 ]

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231

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232 ## filter fragments on relative intensity seuil_ra = user defined

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233 ## parameter (MSpurity flags could be used here)

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234 sfrgtfil <- sfrgt[sfrgt$ra > seuil_ra, ]

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235

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236 mznominal <- round(x = sfrgtfil$mz, mzdecimal)

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237 sfrgtfil <- data.frame(sfrgtfil, mznominal)

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238

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239 ## creation of cross table row=scan col=mz X=ra

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240 vmz <- levels(as.factor(sfrgtfil$mznominal))

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241

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242 cat(" fragments :", vmz)

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243

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244 ## mz of precursor in data precursor to check correlation with

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245 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))

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246

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247 for (m in seq_along(vmz)) {

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248

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249 ## absolute intensity

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250 cln <- c(

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251 which(colnames(sfrgtfil) == "acquisitionNum"),

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252 which(colnames(sfrgtfil) == "i")

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253 )

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254 int_mz <- sfrgtfil[sfrgtfil$mznominal == vmz[m], cln]

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255 colnames(int_mz)[2] <- paste0("mz", vmz[m])

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256

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257 ## average intensities of mass in duplicate scans

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258 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)

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259 int_mz <- comp_scans[, -1]

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260

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261 if (m == 1) {

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262 ds_abs_int <- int_mz

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263 } else {

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264 ds_abs_int <- merge(

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265 x = ds_abs_int,

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266 y = int_mz,

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267 by.x = 1,

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268 by.y = 1,

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269 all.x = TRUE,

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270 all.y = TRUE

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271 )

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272 }

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273 }

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274 if (debug) {

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275 write.table(

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276 x = ds_abs_int,

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277 file = paste0(c_name, "ds_abs_int.txt"),

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278 row.names = FALSE,

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279 sep = "\t"

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280 )

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281 }

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282

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283 ## elimination of mz with less than min_number_scan scans (user defined

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284 ## parameter)

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285 xmz <- rep(NA, ncol(ds_abs_int) - 1)

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286 sum_int <- rep(NA, ncol(ds_abs_int))

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287 nbxmz <- 0

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288 nb_scan_check <- min(nrow(ds_abs_int), min_number_scan)

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289

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290 for (j in 2:ncol(ds_abs_int)) {

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291 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)

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292 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {

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293 nbxmz <- nbxmz + 1

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294 xmz[nbxmz] <- j

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295 }

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296 }

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297

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298 xmz <- xmz[-which(is.na(xmz))]

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299 if (length(xmz) > 0) {

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300 ds_abs_int <- ds_abs_int[, -c(xmz)]

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301 sum_int <- sum_int[-c(xmz)]

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302 ## liste des mz keeped decale de 1 avec ds_abs_int

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303 vmz <- as.numeric(vmz[-c(xmz - 1)])

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304 }

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305

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306 ## reference ion for correlation computing = precursor OR maximum

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307 ## intensity ion in precursor is not present

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308 refcol <- which(colnames(ds_abs_int) == mz_prec)

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309 if (length(refcol) == 0) {

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310 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))

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311 }

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312 pdf(

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313 file = sprintf("%s_processing_file%s.pdf", c_name, mf[f]),

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314 width = 8,

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315 height = 11

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316 )

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317 par(mfrow = c(3, 2))

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diff changeset

318

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319 ## Pearson correlations between absolute intensities computing

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320 cor_abs_int <- rep(NA, length(vmz))

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diff changeset

321

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322 if (length(refcol) > 0) {

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323 for (i in 2:length(ds_abs_int)) {

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324 cor_abs_int[i - 1] <- cor(

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325 x = ds_abs_int[[refcol]],

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326 y = ds_abs_int[[i]],

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327 use = "pairwise.complete.obs",

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328 method = "pearson"

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329 )

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330 plot(

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331 ds_abs_int[[refcol]],

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332 ds_abs_int[[i]],

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333 xlab = colnames(ds_abs_int)[refcol],

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334 ylab = colnames(ds_abs_int)[i],

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335 main = sprintf(

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336 "%s corr coeff r=%s", c_name, round(cor_abs_int[i - 1], 2)

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337 )

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338 )

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339 }

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340 ## plot pseudo spectra

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341 res_comp_by_file <- plot_pseudo_spectra(

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342 x = ds_abs_int,

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343 r_threshold = r_threshold,

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344 fid = mf[f],

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345 sum_int = sum_int,

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346 vmz = vmz,

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347 cor_abs_int = cor_abs_int,

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348 refcol = refcol,

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349 c_name = c_name

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350 )

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351 if (f == 1) {

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352 res_comp <- res_comp_by_file

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353 }

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354 } else {

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355 res_comp_by_file <- NULL

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356 cat(" non detected in fragments file \n")

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357 }

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358 if (!is.null(res_comp_by_file)) {

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359 res_comp <- rbind(res_comp, res_comp_by_file)

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360 }

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361 cat("\n")

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362 dev.off()

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363 }

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364 } else {

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365 res_comp <- NULL

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366 cat(" non detected in precursor file \n")

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367 }

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368 return(res_comp)

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369 }

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370

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371

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372 create_parser <- function() {

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373 parser <- optparse::OptionParser()

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374 parser <- optparse::add_option(

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375 parser,

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376 c("-v", "--verbose"),

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377 action = "store_true",

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378 default = FALSE,

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379 help = "Print extra output [default %default]"

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380 )

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381 parser <- optparse::add_option(

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382 parser,

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383 c("-o", "--output"),

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384 type = "character",

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385 default = DEFAULT_OUTPUT_PATH,

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386 action = "store",

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387 help = "Path to the output file [default %default]"

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388 )

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389 parser <- optparse::add_option(

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390 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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391 c("-p", "--precursors"),

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392 type = "character",

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diff changeset

393 default = DEFAULT_PRECURSOR_PATH,

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394 action = "store",

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395 help = "Path to the precursors file [default %default]"

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diff changeset

396 )

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397 parser <- optparse::add_option(

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398 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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399 c("-f", "--fragments"),

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400 type = "character",

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diff changeset

401 default = DEFAULT_FRAGMENTS_PATH,

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diff changeset

402 action = "store",

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diff changeset

403 help = "Path to the fragments file [default %default]"

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diff changeset

404 )

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diff changeset

405 parser <- optparse::add_option(

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diff changeset

406 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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parents:

diff changeset

407 c("-c", "--compounds"),

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diff changeset

408 type = "character",

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409 default = DEFAULT_COMPOUNDS_PATH,

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410 action = "store",

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diff changeset

411 help = "Path to the compounds file [default %default]"

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diff changeset

412 )

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diff changeset

413 parser <- optparse::add_option(

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414 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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parents:

diff changeset

415 c("--tolmz"),

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parents:

diff changeset

416 type = "numeric",

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workflow4metabolomics

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diff changeset

417 action = "store",

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parents:

diff changeset

418 default = DEFAULT_TOLMZ,

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diff changeset

419 metavar = "number"

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diff changeset

420 )

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workflow4metabolomics

parents:

diff changeset

421 parser <- optparse::add_option(

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workflow4metabolomics

parents:

diff changeset

422 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

423 c("--tolrt"),

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parents:

diff changeset

424 type = "integer",

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workflow4metabolomics

parents:

diff changeset

425 action = "store",

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parents:

diff changeset

426 default = DEFAULT_TOLRT,

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workflow4metabolomics

parents:

diff changeset

427 metavar = "number"

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

428 )

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diff changeset

429 parser <- optparse::add_option(

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workflow4metabolomics

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diff changeset

430 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

431 c("--seuil_ra"),

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workflow4metabolomics

parents:

diff changeset

432 type = "numeric",

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parents:

diff changeset

433 action = "store",

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workflow4metabolomics

parents:

diff changeset

434 help = "relative intensity threshold",

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parents:

diff changeset

435 default = DEFAULT_SEUIL_RA,

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workflow4metabolomics

parents:

diff changeset

436 metavar = "number"

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

437 )

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

438 parser <- optparse::add_option(

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workflow4metabolomics

parents:

diff changeset

439 parser,

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

workflow4metabolomics

parents:

diff changeset

440 c("--mzdecimal"),

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parents:

diff changeset

441 type = "integer",

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workflow4metabolomics

parents:

diff changeset

442 default = DEFAULT_MZDECIMAL,

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workflow4metabolomics

parents:

diff changeset

443 action = "store",

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workflow4metabolomics

parents:

diff changeset

444 help = "nb decimal for mz",

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parents:

diff changeset

445 metavar = "number"

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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diff changeset

446 )

91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"

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parents:

diff changeset

447 parser <- optparse::add_option(

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448 parser,

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449 c("--r_threshold"),

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450 type = "integer",

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451 default = DEFAULT_R_THRESHOLD,

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452 action = "store",

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453 help = paste0(

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454 "r pearson correlation threshold between precursor and fragment ",

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455 "absolute intensity"

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456 ),

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457 metavar = "number"

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458 )

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459 parser <- optparse::add_option(

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460 parser,

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461 c("--min_number_scan"),

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462 type = "numeric",

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463 action = "store",

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464 default = DEFAULT_MINNUMBERSCAN,

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465 help = paste0(

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466 "fragments are kept if there are found in a minimum number ",

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467 "of scans"

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468 ),

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469 metavar = "number"

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470 )

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471 return(parser)

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472 }

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473

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474 main <- function(args) {

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475 ## FOLDER AND FILES

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476 ## MSpurity precursors file

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477 precursors <- read.table(

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478 file = args$precursors,

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479 header = TRUE,

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480 sep = "\t",

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481 quote = "\""

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482 )

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483 ## MSpurity fragments file

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484 fragments <- read.table(

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485 file = args$fragments,

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486 header = TRUE,

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487 sep = "\t",

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488 quote = "\""

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489 )

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490 ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time

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491 compounds <- read.table(

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492 file = args$compounds,

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493 sep = "\t",

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494 quote = "\"",

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495 header = TRUE

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496 )

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497 ## PARAMETERS

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498 ## tolerance for mz(dalton) rt(seconds) to match the standard in the compounds

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499 ## list with the precursor MSpurity file

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500 tolmz <- args$tolmz

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501 tolrt <- args$tolrt

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502

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503 ## relative intensity threshold

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504 seuil_ra <- args$seuil_ra

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505 ## nb decimal for mz

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506 mzdecimal <- args$mzdecimal

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507 ## r pearson correlation threshold between precursor and

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508 # #fragment absolute intensity

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509 r_threshold <- args$r_threshold

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510 ## fragments are kept if there are found in a minimum number of scans

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511 min_number_scan <- args$min_number_scan

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512

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513 for (i in seq_len(nrow(compounds))) {

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514 ## loop execution for all compounds in the compounds file

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515 res_cor <- NULL

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516 res_cor <- extract_fragments(

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517 precursors = precursors,

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518 fragments = fragments,

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519 mzref = compounds[[2]][i],

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520 rtref = compounds[[3]][i],

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521 c_name = compounds[[1]][i],

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522 min_number_scan = min_number_scan,

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523 mzdecimal = mzdecimal,

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524 r_threshold = r_threshold,

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525 seuil_ra = seuil_ra,

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526 tolmz = tolmz,

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527 tolrt = tolrt

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528 )

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529 if (i == 1 & !is.null(res_cor)) {

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530 res_all <- res_cor

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531 } else if (!is.null(res_cor)) {

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532 res_all <- rbind(res_all, res_cor)

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533 }

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534 }

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535

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536 if (is.null(res_all)) {

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537 stop("No result at all!")

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538 }

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539 write.table(

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540 x = res_all,

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541 file = args$output,

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542 sep = "\t",

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543 row.names = FALSE

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544 )

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545 }

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546

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547 args <- optparse::parse_args(create_parser())

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548 sessionInfo()

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549 main(args)

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550

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551 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 0:91a3242fd67f draft