Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 78:b523ce95d857 draft

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author davidvanzessen
date Wed, 11 May 2016 10:29:33 -0400
parents 13c3710604ef
children e39176ccddc8
comparison
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77:c5c86d15cb94 78:b523ce95d857
167 write.table(dat[,mutation.sum.columns], "mutation_by_id.txt", sep="\t",quote=F,row.names=F,col.names=T) 167 write.table(dat[,mutation.sum.columns], "mutation_by_id.txt", sep="\t",quote=F,row.names=F,col.names=T)
168 168
169 setwd(outputdir) 169 setwd(outputdir)
170 170
171 calculate_result = function(i, gene, dat, matrx, f, fname, name){ 171 calculate_result = function(i, gene, dat, matrx, f, fname, name){
172 tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),] 172 tmp = dat[grepl(paste("^", gene, ".*", sep=""), dat$best_match),]
173 173
174 j = i - 1 174 j = i - 1
175 x = (j * 3) + 1 175 x = (j * 3) + 1
176 y = (j * 3) + 2 176 y = (j * 3) + 2
177 z = (j * 3) + 3 177 z = (j * 3) + 3
265 265
266 write.table(x=transitionTable, file=paste("transitions_", name ,"_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA) 266 write.table(x=transitionTable, file=paste("transitions_", name ,"_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA)
267 write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file=paste("matched_", name , "_", fname, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 267 write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file=paste("matched_", name , "_", fname, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
268 268
269 cat(matrx[1,x], file=paste(name, "_", fname, "_value.txt" ,sep="")) 269 cat(matrx[1,x], file=paste(name, "_", fname, "_value.txt" ,sep=""))
270 cat(length(tmp$Sequence.ID), file=paste(name, "_", fname, "_n.txt" ,sep="")) 270 cat(nrow(tmp), file=paste(name, "_", fname, "_n.txt" ,sep=""))
271
272 print(paste(fname, name, nrow(tmp)))
271 273
272 matrx 274 matrx
273 } 275 }
274 276
275 nts = c("a", "c", "g", "t") 277 nts = c("a", "c", "g", "t")