Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/RScript.r @ 17:ee1bda8c27c8 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 09 Nov 2015 08:28:31 -0500 |
| parents | cf1def1aaa74 |
| children | 431797cd74c8 |
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--- a/report_clonality/RScript.r Fri Nov 06 05:12:17 2015 -0500 +++ b/report_clonality/RScript.r Mon Nov 09 08:28:31 2015 -0500 @@ -563,6 +563,7 @@ 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("found IMGT columns, running junction analysis") 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), @@ -587,7 +588,6 @@ 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) @@ -602,18 +602,16 @@ N2=mean(.SD$N2.REGION.nt.nb, na.rm=T), P4=mean(.SD$P5J.nt.nb, na.rm=T), DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), - Total.Del=( mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + - mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + - mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) + - mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)), - - Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) + - mean(.SD$N2.REGION.nt.nb, na.rm=T)), - - Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + - mean(.SD$P5D.nt.nb, na.rm=T) + - mean(.SD$P3D.nt.nb, na.rm=T) + - mean(.SD$P5J.nt.nb, na.rm=T))), + Total.Del=(mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)), + Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) + + mean(.SD$N2.REGION.nt.nb, na.rm=T)), + Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + + mean(.SD$P5D.nt.nb, na.rm=T) + + mean(.SD$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)