Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.r @ 7:ad9be244b104 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 07 Nov 2016 03:04:07 -0500
parents 012a738edf5a
children 3968d04b5724
comparison
equal deleted inserted replaced
6:2ddb9a21f635 7:ad9be244b104
117 117
118 regions = c("FR1", "CDR1", "FR2", "CDR2", "FR3") 118 regions = c("FR1", "CDR1", "FR2", "CDR2", "FR3")
119 if(empty.region.filter == "FR1") { 119 if(empty.region.filter == "FR1") {
120 regions = c("CDR1", "FR2", "CDR2", "FR3") 120 regions = c("CDR1", "FR2", "CDR2", "FR3")
121 } else if (empty.region.filter == "CDR1") { 121 } else if (empty.region.filter == "CDR1") {
122 regions = c("FR2", "CDR2", "FR3", "CDR3") 122 regions = c("FR2", "CDR2", "FR3")
123 } else if (empty.region.filter == "FR2") { 123 } else if (empty.region.filter == "FR2") {
124 regions = c("CDR2", "FR3", "CDR3") 124 regions = c("CDR2", "FR3")
125 } 125 }
126 126
127 sum_by_row = function(x, columns) { sum(as.numeric(x[columns]), na.rm=T) } 127 sum_by_row = function(x, columns) { sum(as.numeric(x[columns]), na.rm=T) }
128 128
129 print("aggregating data into new columns") 129 print("aggregating data into new columns")
227 matrx[9,x] = round(f(tmp$nonSilentMutationsCDR, na.rm=T), digits=1) 227 matrx[9,x] = round(f(tmp$nonSilentMutationsCDR, na.rm=T), digits=1)
228 matrx[9,y] = round(f(tmp$silentMutationsCDR, na.rm=T), digits=1) 228 matrx[9,y] = round(f(tmp$silentMutationsCDR, na.rm=T), digits=1)
229 matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1) 229 matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1)
230 230
231 if(fname == "sum"){ 231 if(fname == "sum"){
232 matrx[10,x] = round(f(rowSums(tmp[,c("FR2.IMGT.Nb.of.nucleotides", "FR3.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1) 232
233 regions.fr = regions[grepl("FR", regions)]
234 regions.fr = paste(regions.fr, ".IMGT.Nb.of.nucleotides", sep="")
235 regions.cdr = regions[grepl("CDR", regions)]
236 regions.cdr = paste(regions.cdr, ".IMGT.Nb.of.nucleotides", sep="")
237
238 if(length(regions.fr) > 1){ #in case there is only on FR region (rowSums needs >1 column)
239 matrx[10,x] = round(f(rowSums(tmp[,regions.fr], na.rm=T)), digits=1)
240 } else {
241 matrx[10,x] = round(f(tmp[,regions.fr], na.rm=T), digits=1)
242 }
233 matrx[10,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1) 243 matrx[10,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
234 matrx[10,z] = round(matrx[10,x] / matrx[10,y] * 100, digits=1) 244 matrx[10,z] = round(matrx[10,x] / matrx[10,y] * 100, digits=1)
235 245
236 matrx[11,x] = round(f(rowSums(tmp[,c("CDR1.IMGT.Nb.of.nucleotides", "CDR2.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1) 246 if(length(regions.cdr) > 1){ #in case there is only on CDR region
247 matrx[11,x] = round(f(rowSums(tmp[,regions.cdr], na.rm=T)), digits=1)
248 } else {
249 matrx[11,x] = round(f(tmp[,regions.cdr], na.rm=T), digits=1)
250 }
237 matrx[11,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1) 251 matrx[11,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
238 matrx[11,z] = round(matrx[11,x] / matrx[11,y] * 100, digits=1) 252 matrx[11,z] = round(matrx[11,x] / matrx[11,y] * 100, digits=1)
239 } 253 }
240 } 254 }
241 255