Mercurial > repos > davidvanzessen > mutation_analysis
changeset 24:31eee1b3d7df draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 07 Apr 2015 05:57:47 -0400 |
| parents | 28b8d980db22 |
| children | 58a62d2c0377 |
| files | mutation_analysis.r |
| diffstat | 1 files changed, 25 insertions(+), 12 deletions(-) [+] |
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--- a/mutation_analysis.r Tue Apr 07 04:46:35 2015 -0400 +++ b/mutation_analysis.r Tue Apr 07 05:57:47 2015 -0400 @@ -130,20 +130,27 @@ totalMutationsAtGC_columns = paste(rep(regions, each=6), c(".IMGT.g.a",".IMGT.c.t",".IMGT.c.a",".IMGT.g.c",".IMGT.c.g",".IMGT.g.t"), sep="") dat$totalMutationsAtGC = apply(dat, FUN=sum_by_row, 1, columns=totalMutationsAtGC_columns) -silentMutations_columns = paste(regions, ".IMGT.Nb.of.silent.mutations", sep="") -silentMutations_columns -dat[,silentMutations_columns] -dat$silentMutations = apply(dat, FUN=sum_by_row, 1, columns=silentMutations_columns) +FRRegions = regions[grepl("FR", regions)] +CDRRegions = regions[grepl("CDR", regions)] + +FR_silentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.silent.mutations", sep="") +dat$silentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_silentMutations_columns) -nonSilentMutations_columns = paste(regions, ".IMGT.Nb.of.nonsilent.mutations", sep="") -dat$nonSilentMutations = apply(dat, FUN=sum_by_row, 1, columns=nonSilentMutations_columns) +CDR_silentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.silent.mutations", sep="") +dat$silentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_silentMutations_columns) + +FR_nonSilentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="") +dat$nonSilentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_nonSilentMutations_columns) + +CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="") +dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns) setwd(outputdir) nts = c("a", "t", "g", "c") zeros=rep(0, 4) -matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=6) +matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=7) for(i in 1:length(genes)){ gene = genes[i] tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),] @@ -169,9 +176,12 @@ matrx[5,x] = sum(tmp$totalMutationsAtGC) matrx[5,y] = sum(tmp$VRegionMutations) matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) - matrx[6,x] = sum(tmp$silentMutations) - matrx[6,y] = sum(tmp$nonSilentMutations) + matrx[6,x] = sum(tmp$silentMutationsFR) + matrx[6,y] = sum(tmp$nonSilentMutationsFR) matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) + matrx[7,x] = sum(tmp$silentMutationsCDR) + matrx[7,y] = sum(tmp$nonSilentMutationsCDR) + matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros) @@ -232,9 +242,12 @@ matrx[5,x] = sum(tmp$totalMutationsAtGC) matrx[5,y] = sum(tmp$VRegionMutations) matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) -matrx[6,x] = sum(tmp$silentMutations) -matrx[6,y] = sum(tmp$nonSilentMutations) +matrx[6,x] = sum(tmp$silentMutationsFR) +matrx[6,y] = sum(tmp$nonSilentMutationsFR) matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) +matrx[7,x] = sum(tmp$silentMutationsCDR) +matrx[7,y] = sum(tmp$nonSilentMutationsCDR) +matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4) row.names(transitionTable) = c("A", "C", "G", "T") @@ -271,7 +284,7 @@ result = data.frame(matrx) -row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "Silent/Non Silent (%)") +row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (%)", "CDR S/R (%)") write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)