Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/RScript.r @ 16:cf1def1aaa74 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 06 Nov 2015 05:12:17 -0500 |
| parents | b45a74248628 |
| children | ee1bda8c27c8 |
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--- a/report_clonality/RScript.r Fri Aug 07 08:42:58 2015 -0400 +++ b/report_clonality/RScript.r Fri Nov 06 05:12:17 2015 -0500 @@ -563,10 +563,6 @@ imgtcolumns = c("X3V.REGION.trimmed.nt.nb","P3V.nt.nb", "N1.REGION.nt.nb", "P5D.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "P3D.nt.nb", "N2.REGION.nt.nb", "P5J.nt.nb", "X5J.REGION.trimmed.nt.nb", "X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb") if(all(imgtcolumns %in% colnames(inputdata))) { - print("MEAN P3V.nt.nb:") - print(PRODF$P3V.nt.nb) - print(mean(PRODF$P3V.nt.nb, na.rm=T)) - print(head(PRODF)) newData = data.frame(data.table(PRODF)[,list(unique=.N, VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), P1=mean(.SD$P3V.nt.nb, na.rm=T), @@ -591,6 +587,8 @@ mean(.SD$P3D.nt.nb, na.rm=T) + mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) + print(newData) + newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) newData = data.frame(data.table(UNPROD)[,list(unique=.N, @@ -617,6 +615,7 @@ mean(.SD$P3D.nt.nb, na.rm=T) + mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) + newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) }