Mercurial > repos > davidvanzessen > shm_csr
changeset 8:3968d04b5724 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 07 Nov 2016 06:52:53 -0500 |
| parents | ad9be244b104 |
| children | 372ccdcf0b2d |
| files | sequence_overview.r shm_csr.r |
| diffstat | 2 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/sequence_overview.r Mon Nov 07 03:04:07 2016 -0500 +++ b/sequence_overview.r Mon Nov 07 06:52:53 2016 -0500 @@ -279,7 +279,9 @@ NTresult = data.frame(nt=c("A", "C", "T", "G")) for(clazz in gene.classes){ + print(paste("class:", clazz)) NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),] + print(paste("nrow:", nrow(NToverview.sub))) new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G)) new.col.y = sum(new.col.x) new.col.z = round(new.col.x / new.col.y * 100, 2)
--- a/shm_csr.r Mon Nov 07 03:04:07 2016 -0500 +++ b/shm_csr.r Mon Nov 07 06:52:53 2016 -0500 @@ -175,6 +175,8 @@ setwd(outputdir) +write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T) + base.order = data.frame(base=c("A", "T", "C", "G"), order=1:4) calculate_result = function(i, gene, dat, matrx, f, fname, name){ @@ -437,8 +439,6 @@ write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T) -write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T) - print("Plotting frequency ranges plot") dat$best_match_class = substr(dat$best_match, 0, 3)