Mercurial > repos > tomnl > msp_split

annotate flag-remove-peaks.R @ 0:aa55ff1d76d4 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit dcfc95273101a7ef0405c2efb8d83f5d456ccd15
author tomnl
date Thu, 10 May 2018 07:20:04 -0400
parents
children 89f33758ad22
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aa55ff1d76d4 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit dcfc95273101a7ef0405c2efb8d83f5d456ccd15
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1 library(XCMSwrapper)
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2 library(optparse)
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3
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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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7 ),
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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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10 ),
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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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13 ),
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14 make_option("--rsd_i_blank", default=NA,
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15 help="RSD threshold for the blank [default = %default]"
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16 ),
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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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19 ),
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20 make_option("--rsd_rt_blank", default=NA,
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21 help="RSD threshold for the RT of the blank [default = %default]"
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22 ),
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23
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24 make_option("--ithres_blank", default=NA,
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25 help="Intensity threshold for the blank [default = %default]"
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26 ),
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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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32 ),
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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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40 ),
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41 make_option("--rsd_i_sample", default=NA,
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42 help="RSD threshold for the samples [default = %default]"
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43 ),
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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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46 ),
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47 make_option("--rsd_rt_sample", default=NA,
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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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56 ),
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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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59 ),
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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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75
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76 make_option("--xset_name", default="xset",
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77 help="Name of the xcmsSet object within the RData file [default = %default]"
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78 )
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79
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80
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81
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82 )
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83
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84 #make_option("--multilist", action="store_true"
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85 # 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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86 #),
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87
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88 # store options
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89 opt<- parse_args(OptionParser(option_list=option_list))
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90
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91 if (is.null(opt$temp_save)){
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92 temp_save<-FALSE
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93 }else{
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94 temp_save<-TRUE
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95 }
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96
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97 if (is.null(opt$remove_spectra)){
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98 remove_spectra<-FALSE
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99 }else{
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100 remove_spectra<-TRUE
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101 }
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102
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103
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104 print(opt)
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105
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106 loadRData <- function(rdata_path, xset_name){
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107 #loads an RData file, and returns the named xset object if it is there
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108 load(rdata_path)
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109 return(get(ls()[ls() == xset_name]))
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110 }
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111
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112 xset<-loadRData(opt$xset_path, opt$xset_name)
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113 print(xset)
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114 if (is.null(opt$samplelist)){
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115 blank_class <- opt$blank_class
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116 }else{
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117 samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)
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118 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes'])
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119
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120 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
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121 if (length(chosen_blank)>1){
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122 print('ERROR: only 1 blank is currently allowed to be used with this tool')
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123 exit()
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124 }
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125 blank_class <- as.character(chosen_blank)
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126 print(blank_class)
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127 }
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128
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129
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130 if (is.null(opt$multilist)){
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131 ffrm_out <- XCMSwrapper::flag_remove(xset,
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132 pol=opt$polarity,
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133 rsd_i_blank=opt$rsd_i_blank,
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134 minfrac_blank=opt$minfrac_blank,
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135 rsd_rt_blank=opt$rsd_rt_blank,
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136 ithres_blank=opt$ithres_blank,
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137 s2b=opt$s2b,
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138 ref.class=blank_class,
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139 egauss_thr=opt$egauss_thr,
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140 rsd_i_sample=opt$rsd_i_sample,
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141 minfrac_sample=opt$minfrac_sample,
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142 rsd_rt_sample=opt$rsd_rt_sample,
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143 ithres_sample=opt$ithres_sample,
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144 minfrac_xcms=opt$minfrac_xcms,
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145 mzwid=opt$mzwid,
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146 bw=opt$bw,
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147 out_dir=opt$out_dir,
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148 temp_save=temp_save,
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149 remove_spectra=remove_spectra,
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150 grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]])
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151
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152 xset <- ffrm_out[[1]]
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153 grp_peaklist <- ffrm_out[[2]]
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154 removed_peaks <- ffrm_out[[3]]
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155
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156 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'))
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157
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158 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
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159 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist),
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160 file.path(opt$out_dir, 'peaklist_filtered.txt'), row.names=FALSE, sep='\t')
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161
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162 removed_peaks <- data.frame(removed_peaks)
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163 write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
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164 file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')
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165
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166 }else{
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167
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168
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169 # TODO
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170 #xsets <- split(xset, multilist_df$multlist)
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171 #
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172 #mult_grps <- unique(multilist_df$multlist)
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173 #
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174 #for (mgrp in mult_grps){
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175 # xset_i <- xsets[mgrp]
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176 # xcms::group(xset_i,
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177 #
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178 # }
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179
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180
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181
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182 }
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183
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184