Mercurial > repos > davidvanzessen > mutation_analysis
comparison mutation_analysis.r @ 40:e022c21f8c47 draft
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) |