Mercurial > repos > computational-metabolomics > mspurity_purityx
comparison flagRemove.R @ 1:0f646a3e0a3f draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
| author | computational-metabolomics |
|---|---|
| date | Thu, 05 Dec 2019 07:36:31 -0500 |
| parents | a141be614e76 |
| children | 6b9a83e08467 |
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| 0:a141be614e76 | 1:0f646a3e0a3f |
|---|---|
| 136 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes']) | 136 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes']) |
| 137 | 137 |
| 138 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] | 138 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] |
| 139 if (length(chosen_blank)>1){ | 139 if (length(chosen_blank)>1){ |
| 140 print('ERROR: only 1 blank is currently allowed to be used with this tool') | 140 print('ERROR: only 1 blank is currently allowed to be used with this tool') |
| 141 exit() | 141 quit() |
| 142 } | 142 } |
| 143 blank_class <- as.character(chosen_blank) | 143 blank_class <- as.character(chosen_blank) |
| 144 print(blank_class) | 144 print(blank_class) |
| 145 } | 145 } |
| 146 | 146 |
| 169 print('flag remove finished') | 169 print('flag remove finished') |
| 170 xset <- ffrm_out[[1]] | 170 xset <- ffrm_out[[1]] |
| 171 grp_peaklist <- ffrm_out[[2]] | 171 grp_peaklist <- ffrm_out[[2]] |
| 172 removed_peaks <- ffrm_out[[3]] | 172 removed_peaks <- ffrm_out[[3]] |
| 173 | 173 |
| 174 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) | 174 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'), version=2) |
| 175 | 175 |
| 176 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) | 176 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) |
| 177 peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv') | 177 peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv') |
| 178 print(peak_pth) | 178 print(peak_pth) |
| 179 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), | 179 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), |