Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 2:2f4298673519 draft

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author davidvanzessen
date Wed, 10 Sep 2014 10:33:29 -0400
parents 74d2bc479bee
children a0b27058dcac
comparison
equal deleted inserted replaced
1:856b5b718d21 2:2f4298673519
292 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F) 292 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)
293 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA) 293 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA)
294 cat(length(dat$Sequence.ID), file="n.txt") 294 cat(length(dat$Sequence.ID), file="n.txt")
295 295
296 296
297 297 weblogo = dat[,c("Sequence.ID", "VGene")]
298 298 weblogo$VGene = gsub("\\*.*", "", weblogo$VGene)
299 299
300 300 rs12 = read.table("HS12RSS.txt", sep="\t", header=TRUE)
301 301 rs23 = read.table("HS23RSS.txt", sep="\t", header=TRUE)
302 302
303 303 result12 = merge(weblogo, rs12, by.x="VGene", by.y="Gene")
304 304 result23 = merge(weblogo, rs23, by.x="VGene", by.y="Gene")
305 305
306 306 write.table(x=result12$Sequence, file="weblogo_in_rs12.txt", sep=",",quote=F,row.names=F,col.names=F)
307 307 write.table(x=result23$Sequence, file="weblogo_in_rs23.txt", sep=",",quote=F,row.names=F,col.names=F)
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