Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 71:9165bec41c02 draft

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Uploaded
author davidvanzessen
date Wed, 04 May 2016 03:48:57 -0400
parents 3636d5aaa127
children 51d92233fb5d
comparison
equal deleted inserted replaced
70:c2e1d5a93f98 71:9165bec41c02
49 "CDR1.IMGT.t.g", 49 "CDR1.IMGT.t.g",
50 "CDR1.IMGT.g.c", 50 "CDR1.IMGT.g.c",
51 "CDR2.IMGT.Nb.of.nucleotides", 51 "CDR2.IMGT.Nb.of.nucleotides",
52 "FR2.IMGT.a.t", 52 "FR2.IMGT.a.t",
53 "CDR1.IMGT.Nb.of.mutations", 53 "CDR1.IMGT.Nb.of.mutations",
54 "CDR3.IMGT.Nb.of.nucleotides",
54 "CDR1.IMGT.a.g", 55 "CDR1.IMGT.a.g",
55 "FR3.IMGT.a.c", 56 "FR3.IMGT.a.c",
56 "FR1.IMGT.g.a", 57 "FR1.IMGT.g.a",
57 "FR3.IMGT.a.g", 58 "FR3.IMGT.a.g",
58 "FR1.IMGT.a.t", 59 "FR1.IMGT.a.t",
220 matrx[8,z] = round(matrx[8,x] / matrx[8,y], digits=1) 221 matrx[8,z] = round(matrx[8,x] / matrx[8,y], digits=1)
221 222
222 matrx[9,x] = round(f(tmp$nonSilentMutationsCDR, na.rm=T), digits=1) 223 matrx[9,x] = round(f(tmp$nonSilentMutationsCDR, na.rm=T), digits=1)
223 matrx[9,y] = round(f(tmp$silentMutationsCDR, na.rm=T), digits=1) 224 matrx[9,y] = round(f(tmp$silentMutationsCDR, na.rm=T), digits=1)
224 matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1) 225 matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1)
226
227 if(fname == "sum"){
228 matrx[10,x] = round(f(rowSums(tmp[,c("FR2.IMGT.Nb.of.nucleotides", "FR3.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1)
229 matrx[10,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
230 matrx[10,z] = round(matrx[10,x] / matrx[10,y], digits=1)
231
232 matrx[11,x] = round(f(rowSums(tmp[,c("CDR1.IMGT.Nb.of.nucleotides", "CDR3.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1)
233 matrx[11,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
234 matrx[11,z] = round(matrx[11,x] / matrx[11,y], digits=1)
235 }
225 } 236 }
226 237
227 transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros) 238 transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros)
228 row.names(transitionTable) = c("A", "C", "G", "T") 239 row.names(transitionTable) = c("A", "C", "G", "T")
229 transitionTable["A","A"] = NA 240 transitionTable["A","A"] = NA
273 284
274 for(i in 1:length(funcs)){ 285 for(i in 1:length(funcs)){
275 func = funcs[[i]] 286 func = funcs[[i]]
276 fname = fnames[[i]] 287 fname = fnames[[i]]
277 288
278 matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=9) 289 rows = 9
290 if(fname == "sum"){
291 rows = 11
292 }
293 matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=rows)
279 294
280 for(i in 1:length(genes)){ 295 for(i in 1:length(genes)){
281 matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i]) 296 matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i])
282 } 297 }
283 298
284 matrx = calculate_result(i + 1, ".*", dat, matrx, func, fname, name="all") 299 matrx = calculate_result(i + 1, ".*", dat, matrx, func, fname, name="all")
285 300
286 result = data.frame(matrx) 301 result = data.frame(matrx)
287 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)") 302 if(fname == "sum"){
303 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR")
304 } else {
305 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)")
306 }
288 307
289 write.table(x=result, file=paste("mutations_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=F) 308 write.table(x=result, file=paste("mutations_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=F)
290 } 309 }
291 310
292 311