Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 25:58a62d2c0377 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Tue, 07 Apr 2015 07:32:43 -0400
parents 31eee1b3d7df
children 2433a1e110e1
comparison
equal deleted inserted replaced
24:31eee1b3d7df 25:58a62d2c0377
174 matrx[4,y] = sum(tmp$totalMutationsAtGC) 174 matrx[4,y] = sum(tmp$totalMutationsAtGC)
175 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1) 175 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1)
176 matrx[5,x] = sum(tmp$totalMutationsAtGC) 176 matrx[5,x] = sum(tmp$totalMutationsAtGC)
177 matrx[5,y] = sum(tmp$VRegionMutations) 177 matrx[5,y] = sum(tmp$VRegionMutations)
178 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) 178 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
179 matrx[6,x] = sum(tmp$silentMutationsFR) 179 matrx[6,x] = sum(tmp$nonSilentMutationsFR)
180 matrx[6,y] = sum(tmp$nonSilentMutationsFR) 180 matrx[6,y] = sum(tmp$silentMutationsFR)
181 matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) 181 matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
182 matrx[7,x] = sum(tmp$silentMutationsCDR) 182 matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
183 matrx[7,y] = sum(tmp$nonSilentMutationsCDR) 183 matrx[7,y] = sum(tmp$silentMutationsCDR)
184 matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) 184 matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
185 185
186 186
187 transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros) 187 transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros)
188 row.names(transitionTable) = c("A", "C", "G", "T") 188 row.names(transitionTable) = c("A", "C", "G", "T")
189 transitionTable["A","A"] = NA 189 transitionTable["A","A"] = NA
240 matrx[4,y] = sum(tmp$totalMutationsAtGC) 240 matrx[4,y] = sum(tmp$totalMutationsAtGC)
241 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1) 241 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1)
242 matrx[5,x] = sum(tmp$totalMutationsAtGC) 242 matrx[5,x] = sum(tmp$totalMutationsAtGC)
243 matrx[5,y] = sum(tmp$VRegionMutations) 243 matrx[5,y] = sum(tmp$VRegionMutations)
244 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) 244 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
245 matrx[6,x] = sum(tmp$silentMutationsFR) 245 matrx[6,x] = sum(tmp$nonSilentMutationsFR)
246 matrx[6,y] = sum(tmp$nonSilentMutationsFR) 246 matrx[6,y] = sum(tmp$silentMutationsFR)
247 matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) 247 matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
248 matrx[7,x] = sum(tmp$silentMutationsCDR) 248 matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
249 matrx[7,y] = sum(tmp$nonSilentMutationsCDR) 249 matrx[7,y] = sum(tmp$silentMutationsCDR)
250 matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) 250 matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
251 251
252 transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4) 252 transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4)
253 row.names(transitionTable) = c("A", "C", "G", "T") 253 row.names(transitionTable) = c("A", "C", "G", "T")
254 transitionTable["A","A"] = NA 254 transitionTable["A","A"] = NA
255 transitionTable["C","C"] = NA 255 transitionTable["C","C"] = NA
282 cat(length(tmp$Sequence.ID), file="total_n.txt") 282 cat(length(tmp$Sequence.ID), file="total_n.txt")
283 283
284 284
285 285
286 result = data.frame(matrx) 286 result = data.frame(matrx)
287 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (%)", "CDR S/R (%)") 287 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (ratio)", "CDR S/R (ratio)")
288 288
289 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F) 289 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)
290 290
291 291
292 if (!("ggplot2" %in% rownames(installed.packages()))) { 292 if (!("ggplot2" %in% rownames(installed.packages()))) {