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annotate flag-remove-peaks.R @ 5:c8db1946f37d draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
author tomnl
date Thu, 03 May 2018 06:59:15 -0400
parents 55aa2dd24828
children ff054daae105
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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1 library(XCMSwrapper)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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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("--xset_name", default="xset",
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75 help="Name of the xcmsSet object within the RData file [default = %default]"
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76 )
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77
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78
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79 )
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80
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81 # store options
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82 opt<- parse_args(OptionParser(option_list=option_list))
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83
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84 if (is.null(opt$temp_save)){
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85 temp_save<-FALSE
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86 }else{
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87 temp_save<-TRUE
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88 }
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89
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90 if (is.null(opt$remove_spectra)){
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91 remove_spectra<-FALSE
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92 }else{
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93 remove_spectra<-TRUE
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94 }
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95
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96
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97 print(opt)
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98
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99 loadRData <- function(rdata_path, xset_name){
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100 #loads an RData file, and returns the named xset object if it is there
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101 load(rdata_path)
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102 return(get(ls()[ls() == xset_name]))
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103 }
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104
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105 xset<-loadRData(opt$xset_path, opt$xset_name)
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106 print(xset)
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107 ffrm_out <- XCMSwrapper::flag_remove(xset,
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108 pol=opt$polarity,
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109 rsd_i_blank=opt$rsd_i_blank,
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110 minfrac_blank=opt$minfrac_blank,
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111 rsd_rt_blank=opt$rsd_rt_blank,
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112 ithres_blank=opt$ithres_blank,
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113 s2b=opt$s2b,
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114 ref.class=opt$blank_class,
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115 egauss_thr=opt$egauss_thr,
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116 rsd_i_sample=opt$rsd_i_sample,
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117 minfrac_sample=opt$minfrac_sample,
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118 rsd_rt_sample=opt$rsd_rt_sample,
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119 ithres_sample=opt$ithres_sample,
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120 minfrac_xcms=opt$minfrac_xcms,
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121 mzwid=opt$mzwid,
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122 bw=opt$bw,
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123 out_dir=opt$out_dir,
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124 temp_save=temp_save,
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125 remove_spectra=remove_spectra,
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126 grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]])
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127
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128 xset <- ffrm_out[[1]]
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129 grp_peaklist <- ffrm_out[[2]]
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130 removed_peaks <- ffrm_out[[3]]
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131
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132 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'))
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133
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134 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
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135 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist),
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136 file.path(opt$out_dir, 'peaklist_filtered.txt'), row.names=FALSE, sep='\t')
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137
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138 removed_peaks <- data.frame(removed_peaks)
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139 write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
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140 file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')