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annotate filterFragSpectra.R @ 9:da36e8bbcfbd draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:35:07 +0000
parents a0ee43397d1e
children
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(optparse)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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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12 make_option("--ilim", default = 0.0),
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13 make_option("--plim", default = 0.0),
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14 make_option("--ra", default = 0.0),
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15 make_option("--snr", default = 0.0),
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16 make_option("--rmp", action = "store_true"),
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17 make_option("--snmeth", default = "median", type = "character"),
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18 make_option("--allfrag", action = "store_true")
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19 )
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21 opt <- parse_args(OptionParser(option_list = option_list))
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22 print(opt)
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25 loadRData <- function(rdata_path, name) {
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26 # loads an RData file, and returns the named xset object if it is there
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27 load(rdata_path)
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28 return(get(ls()[ls() %in% name]))
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29 }
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31 # Requires
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32 pa <- loadRData(opt$pa, "pa")
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34 if (is.null(opt$rmp)) {
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35 opt$rmp <- FALSE
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36 } else {
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37 opt$rmp <- TRUE
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38 }
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39
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40 if (is.null(opt$allfrag)) {
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41 opt$allfrag <- FALSE
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42 } else {
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43 opt$allfrag <- TRUE
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44 }
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46 pa <- filterFragSpectra(pa,
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47 ilim = opt$ilim,
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48 plim = opt$plim,
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49 ra = opt$ra,
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50 snr = opt$snr,
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51 rmp = opt$rmp,
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52 allfrag = opt$allfrag,
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53 snmeth = opt$snmeth
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54 )
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56 print(pa)
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57 save(pa, file = opt$out_rdata)
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59 # get the msms data for grpid from the purityA object
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60 msmsgrp <- function(grpid, pa) {
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61 msms <- pa@grped_ms2[grpid]
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63 grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
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65 grpinfo$subsetid <- seq_len(nrow(grpinfo))
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66 result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
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67 return(result)
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68 }
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69
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70 # Set the relevant details
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71 setid <- function(grpinfo_i, msms) {
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72 msms_i <- msms[[1]][[grpinfo_i$subsetid]]
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73 n <- nrow(msms_i)
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74 msms_i <- data.frame(msms_i)
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75 colnames(msms_i)[1:2] <- c("mz", "i")
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76 m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
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77 return(m)
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78 }
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81
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82 if (length(pa) > 0) {
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83 if (length(pa@grped_ms2) == 0) {
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84 message("No spectra available")
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85 } else {
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86 # get group ids
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87 grpids <- unique(as.character(pa@grped_df$grpid))
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89 # loop through all the group ids
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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90 df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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91 df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
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a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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93 # select and reorder columns
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94 df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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96 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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98 print(head(pa@grped_df))
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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99 write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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100 print(head(df_fragments))
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a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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101 write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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103 }