Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 68:3636d5aaa127 draft

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author davidvanzessen
date Wed, 20 Apr 2016 10:16:25 -0400
parents 7290a88ea202
children 9165bec41c02
comparison
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67:67a9ddf6a8f5 68:3636d5aaa127
170 170
171 setwd(outputdir) 171 setwd(outputdir)
172 172
173 173
174 calculate_result = function(i, gene, dat, matrx, f, fname, name){ 174 calculate_result = function(i, gene, dat, matrx, f, fname, name){
175 tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),] 175 tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),]
176 176
177 j = i - 1 177 j = i - 1
178 x = (j * 3) + 1 178 x = (j * 3) + 1
179 y = (j * 3) + 2 179 y = (j * 3) + 2
180 z = (j * 3) + 3 180 z = (j * 3) + 3
181 181
182 if(nrow(tmp) > 0){ 182 if(nrow(tmp) > 0){
183 183
184 matrx[1,x] = round(f(tmp$VRegionMutations, na.rm=T), digits=1) 184 if(fname == "sum"){
185 matrx[1,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1) 185 matrx[1,x] = round(f(tmp$VRegionMutations, na.rm=T), digits=1)
186 matrx[1,z] = round(matrx[1,x] / matrx[1,y] * 100, digits=1) 186 matrx[1,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
187 matrx[1,z] = round(f(matrx[1,x] / matrx[1,y]) * 100, digits=1)
188 } else {
189 matrx[1,x] = round(f(tmp$VRegionMutations, na.rm=T), digits=1)
190 matrx[1,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
191 matrx[1,z] = round(f(tmp$VRegionMutations / tmp$VRegionNucleotides) * 100, digits=1)
192 }
187 193
188 matrx[2,x] = round(f(tmp$transitionMutations, na.rm=T), digits=1) 194 matrx[2,x] = round(f(tmp$transitionMutations, na.rm=T), digits=1)
189 matrx[2,y] = round(f(tmp$VRegionMutations, na.rm=T), digits=1) 195 matrx[2,y] = round(f(tmp$VRegionMutations, na.rm=T), digits=1)
190 matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1) 196 matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1)
191 197