Mercurial > repos > tomnl > mspurity_createmsp

comparison averageFragSpectra.R @ 15:70257c77ea04 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:34:20 +0000
parents df2efceff4cd
children
comparison
equal deleted inserted replaced
14:998c58a7abb3 15:70257c77ea04
142 if (nrow(av_spectra)==0){ 142 if (nrow(av_spectra)==0){
143 message('No average spectra available') 143 message('No average spectra available')
144 } else{ 144 } else{
145 colnames(av_spectra)[1] <- 'grpid' 145 colnames(av_spectra)[1] <- 'grpid'
146 av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid] 146 av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
147
148 if((length(pa@av_intra_params)>0) || (length(pa@av_inter_params)>0) ){
149 # Add some extra info (only required if av_intra or av_inter performed)
150 colnames(av_spectra)[2] <- 'fileid'
151 av_spectra$avid <- 1:nrow(av_spectra)
152
153 filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)])
154 # filenames_galaxy <- sapply(av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
155
156 av_spectra = as.data.frame(append(av_spectra, list(filename = filenames), after=2))
157 }
147 158
148 colnames(av_spectra)[2] <- 'fileid'
149 av_spectra$avid <- 1:nrow(av_spectra)
150
151 filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)])
152 # filenames_galaxy <- sapply(av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
153
154 av_spectra = as.data.frame(append(av_spectra, list(filename = filenames), after=2))
155 159
156 print(head(av_spectra)) 160 print(head(av_spectra))
157 write.table(av_spectra, opt$out_peaklist, row.names=FALSE, sep='\t') 161 write.table(av_spectra, opt$out_peaklist, row.names=FALSE, sep='\t')
158 162
159 } 163 }