Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 40:e022c21f8c47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 07:10:36 -0500
parents ac9a4307861a
children 9afd8430de2c
comparison
equal deleted inserted replaced
39:7377bf7e632d 40:e022c21f8c47
143 dat$nonSilentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_nonSilentMutations_columns) 143 dat$nonSilentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_nonSilentMutations_columns)
144 144
145 CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="") 145 CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="")
146 dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns) 146 dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns)
147 147
148 mutation.sum.columns = c("Sequence.ID", "VRegionMutations", "VRegionNucleotides", "transitionMutations", "transversionMutations", "transitionMutationsAtGC", "silentMutationsFR", "nonSilentMutationsFR", "silentMutationsCDR", "nonSilentMutationsCDR")
149
150 write.table(dat[,mutation.sum.columns], "mutation_by_id.txt", sep="\t",quote=F,row.names=F,col.names=T)
148 151
149 setwd(outputdir) 152 setwd(outputdir)
150 153
151 nts = c("a", "c", "g", "t") 154 nts = c("a", "c", "g", "t")
152 zeros=rep(0, 4) 155 zeros=rep(0, 4)