Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

annotate filterFragSpectra.R @ 7:2e10c13085c9 draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author computational-metabolomics
date Tue, 08 Feb 2022 14:02:03 +0000
parents cc0f8ddad4a8
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1 library(optparse)
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2 library(msPurity)
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3 library(xcms)
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4 print(sessionInfo())
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7 option_list <- list(
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8 make_option("--out_rdata", type = "character"),
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9 make_option("--out_peaklist_prec", type = "character"),
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10 make_option("--out_peaklist_frag", type = "character"),
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11 make_option("--pa", type = "character"),
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13 make_option("--ilim", default = 0.0),
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14 make_option("--plim", default = 0.0),
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16 make_option("--ra", default = 0.0),
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17 make_option("--snr", default = 0.0),
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19 make_option("--rmp", action = "store_true"),
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20 make_option("--snmeth", default = "median", type = "character"),
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21 make_option("--allfrag", action = "store_true")
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22 )
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24 opt <- parse_args(OptionParser(option_list = option_list))
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25 print(opt)
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28 loadRData <- function(rdata_path, name) {
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29 #loads an RData file, and returns the named xset object if it is there
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30 load(rdata_path)
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31 return(get(ls()[ls() %in% name]))
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32 }
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34 # Requires
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35 pa <- loadRData(opt$pa, "pa")
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37 if (is.null(opt$rmp)) {
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38 opt$rmp <- FALSE
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39 }else{
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40 opt$rmp <- TRUE
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41 }
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42
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43 if (is.null(opt$allfrag)) {
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44 opt$allfrag <- FALSE
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45 }else{
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46 opt$allfrag <- TRUE
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47 }
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48
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49 pa <- filterFragSpectra(pa,
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50 ilim = opt$ilim,
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51 plim = opt$plim,
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52 ra = opt$ra,
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53 snr = opt$snr,
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54 rmp = opt$rmp,
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55 allfrag = opt$allfrag,
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56 snmeth = opt$snmeth)
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58 print(pa)
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59 save(pa, file = opt$out_rdata)
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61 # get the msms data for grpid from the purityA object
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62 msmsgrp <- function(grpid, pa) {
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63 msms <- pa@grped_ms2[grpid]
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65 grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
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67 grpinfo$subsetid <- seq_len(nrow(grpinfo))
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68 result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
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69 return(result)
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70 }
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72 # Set the relevant details
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73 setid <- function(grpinfo_i, msms) {
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74 msms_i <- msms[[1]][[grpinfo_i$subsetid]]
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75 n <- nrow(msms_i)
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76 msms_i <- data.frame(msms_i)
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77 colnames(msms_i)[1:2] <- c("mz", "i")
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78 m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
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79 return(m)
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80 }
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84 if (length(pa) > 0) {
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86 if (length(pa@grped_ms2) == 0) {
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87 message("No spectra available")
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88 } else {
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89
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90 # get group ids
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91 grpids <- unique(as.character(pa@grped_df$grpid))
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92
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93 # loop through all the group ids
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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95 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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96 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97 #select and reorder columns
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98 df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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100 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
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101
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102 print(head(pa@grped_df))
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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103 write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
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104 print(head(df_fragments))
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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105 write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
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106 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107 }