Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

annotate purityX.R @ 11:0a0f22586cad draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a
author computational-metabolomics
date Fri, 13 Sep 2024 13:36:00 +0000
parents 06bfdbee9b47
children
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1 library(msPurity)
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2 library(optparse)
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3 print(sessionInfo())
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5 option_list <- list(
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6 make_option(c("--xset_path"), type = "character"),
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7 make_option(c("-o", "--out_dir"), type = "character"),
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8 make_option(c("--mzML_path"), type = "character"),
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9 make_option("--minOffset", default = 0.5),
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10 make_option("--maxOffset", default = 0.5),
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11 make_option("--ilim", default = 0.05),
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12 make_option("--iwNorm", default = "none", type = "character"),
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13 make_option("--exclude_isotopes", action = "store_true"),
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14 make_option("--isotope_matrix", type = "character"),
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15 make_option("--purityType", default = "purityFWHMmedian"),
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16 make_option("--singleFile", default = 0),
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17 make_option("--cores", default = 4),
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18 make_option("--xgroups", type = "character"),
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19 make_option("--camera_xcms", default = "xset"),
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20 make_option("--files", type = "character"),
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21 make_option("--galaxy_files", type = "character"),
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22 make_option("--choose_class", type = "character"),
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23 make_option("--ignore_files", type = "character"),
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24 make_option("--rtraw_columns", action = "store_true")
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25 )
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28 opt <- parse_args(OptionParser(option_list = option_list))
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29 print(opt)
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32 if (!is.null(opt$xgroups)) {
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33 xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]])
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34 } else {
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35 xgroups <- NULL
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36 }
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39 print(xgroups)
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41 if (!is.null(opt$remove_nas)) {
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42 df <- df[!is.na(df$mz), ]
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43 }
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45 if (is.null(opt$isotope_matrix)) {
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46 im <- NULL
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47 } else {
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48 im <- read.table(opt$isotope_matrix,
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49 header = TRUE, sep = "\t", stringsAsFactors = FALSE
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50 )
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51 }
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53 if (is.null(opt$exclude_isotopes)) {
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54 isotopes <- FALSE
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55 } else {
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56 isotopes <- TRUE
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57 }
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59 if (is.null(opt$rtraw_columns)) {
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60 rtraw_columns <- FALSE
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61 } else {
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62 rtraw_columns <- TRUE
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63 }
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64
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65 loadRData <- function(rdata_path, xnames) {
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66 # loads an RData file, and returns the named xset object if it is there
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67 load(rdata_path)
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68 return(get(ls()[ls() %in% xnames]))
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69 }
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74 getxcmsSetObject <- function(xobject) {
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75 # XCMS 1.x
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76 if (class(xobject) == "xcmsSet"){
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77 return(xobject)
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78 }
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79 # XCMS 3.x
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80 if (class(xobject) == "XCMSnExp") {
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81 # Get the legacy xcmsSet object
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82 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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83 if (!is.null(xset@phenoData$sample_group)){
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84 xcms::sampclass(xset) <- xset@phenoData$sample_group
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85 }else{
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86 xcms::sampclass(xset) <- "."
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87 }
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88 return(xset)
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89 }
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90 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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91
10
06bfdbee9b47 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5
computational-metabolomics
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diff changeset
92 target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata'))
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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93
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 0
diff changeset
94 if (opt$camera_xcms == "camera") {
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
95 xset <- target_obj@xcmsSet
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
96 } else {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
97 xset <- target_obj
0
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"
computational-metabolomics
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99
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
100 xset <- getxcmsSetObject(xset)
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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101
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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102 print(xset)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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103
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 0
diff changeset
104 minOffset <- as.numeric(opt$minOffset)
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
105 maxOffset <- as.numeric(opt$maxOffset)
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106
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cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
107 if (opt$iwNorm == "none") {
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
108 iwNorm <- FALSE
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
109 iwNormFun <- NULL
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
110 } else if (opt$iwNorm == "gauss") {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
111 iwNorm <- TRUE
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
112 iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
113 } else if (opt$iwNorm == "rcosine") {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
114 iwNorm <- TRUE
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
115 iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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116 } else if (opt$iwNorm == "QE5") {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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117 iwNorm <- TRUE
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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118 iwNormFun <- msPurity::iwNormQE.5()
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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120
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121 print(xset@filepaths)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122
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computational-metabolomics
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123 if (!is.null(opt$files)) {
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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124 updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]])
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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125 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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126 print(updated_filepaths)
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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127 updated_filenames <- basename(updated_filepaths)
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
128 original_filenames <- basename(xset@filepaths)
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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129 update_idx <- match(updated_filenames, original_filenames)
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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130
8
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131 if (!is.null(opt$galaxy_files)) {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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132 galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]])
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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133 galaxy_files <- galaxy_files[galaxy_files != ""]
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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134 xset@filepaths <- galaxy_files[update_idx]
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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135 } else {
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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136 xset@filepaths <- updated_filepaths[update_idx]
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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137 }
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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138 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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140 if (!is.null(opt$choose_class)) {
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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141 classes <- trimws(strsplit(opt$choose_class, ",")[[1]])
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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142
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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143 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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diff changeset
145 print("choose class")
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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146 print(ignore_files_class)
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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147 } else {
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 ignore_files_class <- NA
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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149 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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150
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151 if (!is.null(opt$ignore_files)) {
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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152 ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]])
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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153 filenames <- rownames(xset@phenoData)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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154 ignore_files <- which(filenames %in% ignore_files_string)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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155
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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156 ignore_files <- unique(c(ignore_files, ignore_files_class))
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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157 ignore_files <- ignore_files[ignore_files != ""]
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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diff changeset
158 } else {
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
159 if (anyNA(ignore_files_class)) {
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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160 ignore_files <- NULL
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
161 } else {
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
162 ignore_files <- ignore_files_class
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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163 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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164 }
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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165
6
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
166 print("ignore_files")
0
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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diff changeset
167 print(ignore_files)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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168
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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169
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
170 ppLCMS <- msPurity::purityX(
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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diff changeset
171 xset = xset,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
172 offsets = c(minOffset, maxOffset),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
173 cores = opt$cores,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
174 xgroups = xgroups,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
175 purityType = opt$purityType,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
176 ilim = opt$ilim,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
177 isotopes = isotopes,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
178 im = im,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
179 iwNorm = iwNorm,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
180 iwNormFun = iwNormFun,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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181 singleFile = opt$singleFile,
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182 fileignore = ignore_files,
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183 rtrawColumns = rtraw_columns
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184 )
0
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185
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186 dfp <- ppLCMS@predictions
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187
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188 # to make compatable with deconrank
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189 # (keep grpid for other compatibility)
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190 dfp <- data.frame("peakID"=dfp$grpid, dfp)
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191
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192 colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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193 colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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194 colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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195 colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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196 colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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197 colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity"
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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198
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199 if (sum(is.na(dfp$medianPurity)) > 0) {
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200 dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0
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201 }
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202
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203 print(head(dfp))
cc0f8ddad4a8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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204 write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t")
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205
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206 save.image(file.path(opt$out_dir, "purityX_output.RData"))