Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

annotate filterFragSpectra.R @ 6:cc0f8ddad4a8 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:28:18 +0000
parents 96af79da0cc6
children 2e10c13085c9
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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 )
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23 opt <- parse_args(OptionParser(option_list = option_list))
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24 print(opt)
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27 loadRData <- function(rdata_path, name) {
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28 #loads an RData file, and returns the named xset object if it is there
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29 load(rdata_path)
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30 return(get(ls()[ls() %in% name]))
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31 }
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33 # Requires
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34 pa <- loadRData(opt$pa, "pa")
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36 if (is.null(opt$rmp)) {
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37 opt$rmp <- FALSE
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38 }else{
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39 opt$rmp <- TRUE
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40 }
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42 pa <- filterFragSpectra(pa,
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43 ilim = opt$ilim,
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44 plim = opt$plim,
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45 ra = opt$ra,
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46 snr = opt$snr,
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47 rmp = opt$rmp,
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48 snmeth = opt$snmeth)
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50 print(pa)
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51 save(pa, file = opt$out_rdata)
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53 # get the msms data for grpid from the purityA object
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54 msmsgrp <- function(grpid, pa) {
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55 msms <- pa@grped_ms2[grpid]
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57 grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
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59 grpinfo$subsetid <- seq_len(nrow(grpinfo))
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60 result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
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61 return(result)
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62 }
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64 # Set the relevant details
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65 setid <- function(grpinfo_i, msms) {
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66 msms_i <- msms[[1]][[grpinfo_i$subsetid]]
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67 n <- nrow(msms_i)
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68 msms_i <- data.frame(msms_i)
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69 colnames(msms_i)[1:2] <- c("mz", "i")
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70 m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
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71 return(m)
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72 }
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76 if (length(pa) > 0) {
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78 if (length(pa@grped_ms2) == 0) {
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79 message("No spectra available")
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80 } else {
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82 # get group ids
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83 grpids <- unique(as.character(pa@grped_df$grpid))
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85 # loop through all the group ids
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86 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
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87 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
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88 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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89 #select and reorder columns
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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90 df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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93
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94 print(head(pa@grped_df))
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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95 write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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96 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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97 write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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98 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99 }