Mercurial > repos > computational-metabolomics > mspurity_purityx

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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 13:57:32 +0000
parents 6b9a83e08467
children b16952cc06d2
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a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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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4 option_list <- list(
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5 make_option(c("-o", "--out_dir"), type = "character", default = getwd(),
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6 help = "Output folder for resulting files [default = %default]"
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8 make_option(c("-x", "--xset_path"), type = "character", default = file.path(getwd(), "xset.rds"),
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9 help = "The path to the xcmsSet object [default = %default]"
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11 make_option("--polarity", default = NA,
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12 help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
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14 make_option("--rsd_i_blank", default = 100,
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15 help = "RSD threshold for the blank [default = %default]"
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17 make_option("--minfrac_blank", default = 0.5,
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18 help = "minimum fraction of files for features needed for the blank [default = %default]"
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20 make_option("--rsd_rt_blank", default = 100,
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21 help = "RSD threshold for the RT of the blank [default = %default]"
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24 make_option("--ithres_blank", default = 0,
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25 help = "Intensity threshold for the blank [default = %default]"
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27 make_option("--s2b", default = 10,
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28 help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.
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29 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
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30 1000/10 = 100, so sample has fold change higher than the threshold and the peak
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31 is not considered a blank [default = %default]"
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33 make_option("--blank_class", default = "blank", type = "character",
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34 help = "A string representing the class that will be used for the blank.[default = %default]"
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35 ),
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36 make_option("--egauss_thr", default = NA,
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37 help = "Threshold for filtering out non gaussian shaped peaks. Note this only works
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38 if the 'verbose columns' and 'fit gauss' was used with xcms
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39 [default = %default]"
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41 make_option("--rsd_i_sample", default = 100,
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42 help = "RSD threshold for the samples [default = %default]"
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44 make_option("--minfrac_sample", default = 0.8,
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45 help = "minimum fraction of files for features needed for the samples [default = %default]"
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47 make_option("--rsd_rt_sample", default = 100,
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48 help = "RSD threshold for the RT of the samples [default = %default]"
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49 ),
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50 make_option("--ithres_sample", default = 5000,
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51 help = "Intensity threshold for the sample [default = %default]"
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52 ),
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53 make_option("--grp_rm_ids", default = NA,
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54 help = "vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
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55 [default = %default]"
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57 make_option("--remove_spectra", action = "store_true",
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58 help = "TRUE if flagged spectra is to be removed [default = %default]"
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60 make_option("--minfrac_xcms", default = 0.5,
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61 help = "minfrac for xcms grouping [default = %default]"
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62 ),
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63 make_option("--mzwid", default = 0.001,
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64 help = "mzwid for xcms grouping [default = %default]"
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65 ),
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66 make_option("--bw", default = 5,
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67 help = "bw for xcms grouping [default = %default]"
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68 ),
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69
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70 make_option("--temp_save", action = "store_true",
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71 help = "Assign True if files for each step saved (for testing purposes) [default = %default]"
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72 ),
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73
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74 make_option("--samplelist", type = "character", help = "Sample list to determine the blank class")
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76 )
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77
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78 # nolint start
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79 # make_option("--multilist", action="store_true"
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80 # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided"
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81 # ),
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82 # nolint end
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84 # store options
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85 opt <- parse_args(OptionParser(option_list = option_list))
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87 opt <- replace(opt, opt == "NA", NA)
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88
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89 if (is.null(opt$temp_save)) {
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90 temp_save <- FALSE
0
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91 }else{
6
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92 temp_save <- TRUE
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93 }
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94
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95 if (is.null(opt$remove_spectra)) {
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96 remove_spectra <- FALSE
0
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97 }else{
6
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98 remove_spectra <- TRUE
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99 }
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100
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101
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102 print(opt)
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103
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104 getxcmsSetObject <- function(xobject) {
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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105 # XCMS 1.x
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106 if (class(xobject) == "xcmsSet")
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107 return(xobject)
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108 # XCMS 3.x
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109 if (class(xobject) == "XCMSnExp") {
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110 # Get the legacy xcmsSet object
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111 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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112 xcms::sampclass(xset) <- xset@phenoData$sample_group
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113 return(xset)
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114 }
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115 }
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116
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117
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118 loadRData <- function(rdata_path, name) {
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119 #loads an RData file, and returns the named xset object if it is there
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120 load(rdata_path)
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121 return(get(ls()[ls() %in% name]))
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122 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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123
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124 xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))
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125
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126 print(xset)
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127 if (is.null(opt$samplelist)) {
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128 blank_class <- opt$blank_class
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129 }else{
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130 samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
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131 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])
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132
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133 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
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134 if (length(chosen_blank) > 1) {
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135 print("ERROR: only 1 blank is currently allowed to be used with this tool")
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136 quit()
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137 }
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138 blank_class <- as.character(chosen_blank)
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139 print(blank_class)
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140 }
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141
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142
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143 if (is.null(opt$multilist)) {
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144 ffrm_out <- flag_remove(xset,
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145 pol = opt$polarity,
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146 rsd_i_blank = opt$rsd_i_blank,
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147 minfrac_blank = opt$minfrac_blank,
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148 rsd_rt_blank = opt$rsd_rt_blank,
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149 ithres_blank = opt$ithres_blank,
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150 s2b = opt$s2b,
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151 ref.class = blank_class,
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152 egauss_thr = opt$egauss_thr,
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153 rsd_i_sample = opt$rsd_i_sample,
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154 minfrac_sample = opt$minfrac_sample,
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155 rsd_rt_sample = opt$rsd_rt_sample,
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156 ithres_sample = opt$ithres_sample,
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157 minfrac_xcms = opt$minfrac_xcms,
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158 mzwid = opt$mzwid,
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159 bw = opt$bw,
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160 out_dir = opt$out_dir,
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161 temp_save = temp_save,
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162 remove_spectra = remove_spectra,
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163 grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]])
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164 print("flag remove finished")
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165 xset <- ffrm_out[[1]]
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166 grp_peaklist <- ffrm_out[[2]]
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167 removed_peaks <- ffrm_out[[3]]
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168
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169 save.image(file = file.path(opt$out_dir, "xset_filtered.RData"), version = 2)
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170
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171 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
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172 peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")
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173 print(peak_pth)
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174 write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),
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175 peak_pth, row.names = FALSE, sep = "\t")
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176
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177 removed_peaks <- data.frame(removed_peaks)
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178 write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
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179 file.path(opt$out_dir, "removed_peaks.tsv"), row.names = FALSE, sep = "\t")
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180
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181 }else{
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182
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183 # nolint start
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184 # TODO
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185 #xsets <- split(xset, multilist_df$multlist)
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186 #
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187 #mult_grps <- unique(multilist_df$multlist)
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188 #
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189 #for (mgrp in mult_grps){
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190 # xset_i <- xsets[mgrp]
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191 # xcms::group(xset_i,
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192 #
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193 # }
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194 # nolint end
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195
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196
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197 }