Mercurial > repos > davidvanzessen > mutation_analysis
diff mutation_analysis.r @ 25:58a62d2c0377 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 07 Apr 2015 07:32:43 -0400 |
| parents | 31eee1b3d7df |
| children | 2433a1e110e1 |
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--- a/mutation_analysis.r Tue Apr 07 05:57:47 2015 -0400 +++ b/mutation_analysis.r Tue Apr 07 07:32:43 2015 -0400 @@ -176,12 +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$silentMutationsFR) - matrx[6,y] = sum(tmp$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) + matrx[6,x] = sum(tmp$nonSilentMutationsFR) + matrx[6,y] = sum(tmp$silentMutationsFR) + matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1) + matrx[7,x] = sum(tmp$nonSilentMutationsCDR) + matrx[7,y] = sum(tmp$silentMutationsCDR) + matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1) transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros) @@ -242,12 +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$silentMutationsFR) -matrx[6,y] = sum(tmp$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) +matrx[6,x] = sum(tmp$nonSilentMutationsFR) +matrx[6,y] = sum(tmp$silentMutationsFR) +matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1) +matrx[7,x] = sum(tmp$nonSilentMutationsCDR) +matrx[7,y] = sum(tmp$silentMutationsCDR) +matrx[7,z] = round(matrx[7,x] / matrx[7,y], 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") @@ -284,7 +284,7 @@ result = data.frame(matrx) -row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (%)", "CDR S/R (%)") +row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (ratio)", "CDR S/R (ratio)") write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)