Mercurial > repos > davidvanzessen > shm_csr

comparison merge_and_filter.r @ 96:385dea3c6cb5 draft

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planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5
author rhpvorderman
date Fri, 05 Jan 2024 08:53:22 +0000
parents 8fcf31272f6e
children
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95:d63eff357515 96:385dea3c6cb5
181 } else if(empty.region.filter == "CDR1"){ 181 } else if(empty.region.filter == "CDR1"){
182 result = result[result$FR2.IMGT.seq != "" & result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ] 182 result = result[result$FR2.IMGT.seq != "" & result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
183 } else if(empty.region.filter == "FR2"){ 183 } else if(empty.region.filter == "FR2"){
184 result = result[result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ] 184 result = result[result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ]
185 } 185 }
186 # If empty region filter is None, nothing happens.
186 187
187 print(paste("After removal sequences that are missing a gene region:", nrow(result))) 188 print(paste("After removal sequences that are missing a gene region:", nrow(result)))
188 filtering.steps = rbind(filtering.steps, c("After removal sequences that are missing a gene region", nrow(result))) 189 filtering.steps = rbind(filtering.steps, c("After removal sequences that are missing a gene region", nrow(result)))
189 190
190 if(empty.region.filter == "leader"){ 191 if(empty.region.filter == "leader"){
217 218
218 if(filter.unique != "no"){ 219 if(filter.unique != "no"){
219 clmns = names(result) 220 clmns = names(result)
220 if(filter.unique == "remove_vjaa"){ 221 if(filter.unique == "remove_vjaa"){
221 result$unique.def = paste(result$VGene, result$JGene, result$CDR3.IMGT.AA) 222 result$unique.def = paste(result$VGene, result$JGene, result$CDR3.IMGT.AA)
222 } else if(empty.region.filter == "leader"){ 223 } else if(empty.region.filter == "leader" || empty.region.filter == "None"){
223 result$unique.def = paste(result$FR1.IMGT.seq, result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) 224 result$unique.def = paste(result$FR1.IMGT.seq, result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq)
224 } else if(empty.region.filter == "FR1"){ 225 } else if(empty.region.filter == "FR1"){
225 result$unique.def = paste(result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) 226 result$unique.def = paste(result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq)
226 } else if(empty.region.filter == "CDR1"){ 227 } else if(empty.region.filter == "CDR1"){
227 result$unique.def = paste(result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) 228 result$unique.def = paste(result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq)