Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/RScript.r @ 55:67627d77d63b draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 16 Mar 2016 11:17:49 -0400 |
| parents | 5ba0377b7737 |
| children |
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--- a/report_clonality/RScript.r Fri Jan 29 08:10:21 2016 -0500 +++ b/report_clonality/RScript.r Wed Mar 16 11:17:49 2016 -0400 @@ -646,6 +646,8 @@ PRODF$N1.REGION.nt.nb = PRODF$N.REGION.nt.nb } + num_median = function(x, na.rm) { as.numeric(median(x, na.rm=na.rm)) } + 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), @@ -671,7 +673,32 @@ mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) - write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + write.table(newData, "junctionAnalysisProd_mean.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + + newData = data.frame(data.table(PRODF)[,list(unique=.N, + VH.DEL=num_median(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), + P1=num_median(.SD$P3V.nt.nb, na.rm=T), + N1=num_median(.SD$N1.REGION.nt.nb, na.rm=T), + P2=num_median(.SD$P5D.nt.nb, na.rm=T), + DEL.DH=num_median(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T), + DH.DEL=num_median(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T), + P3=num_median(.SD$P3D.nt.nb, na.rm=T), + N2=num_median(.SD$N2.REGION.nt.nb, na.rm=T), + P4=num_median(.SD$P5J.nt.nb, na.rm=T), + DEL.JH=num_median(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), + Total.Del=num_median(c(.SD$X3V.REGION.trimmed.nt.nb, + .SD$X5D.REGION.trimmed.nt.nb, + .SD$X3D.REGION.trimmed.nt.nb, + .SD$X5J.REGION.trimmed.nt.nb), na.rm=T), + Total.N=num_median( c(.SD$N1.REGION.nt.nb, + .SD$N2.REGION.nt.nb), na.rm=T), + Total.P=num_median(c(.SD$P3V.nt.nb, + .SD$P5D.nt.nb, + .SD$P3D.nt.nb, + .SD$P5J.nt.nb), na.rm=T)), + by=c("Sample")]) + newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) + write.table(newData, "junctionAnalysisProd_median.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) newData = data.frame(data.table(UNPROD)[,list(unique=.N, VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), @@ -696,7 +723,33 @@ mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) - write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + write.table(newData, "junctionAnalysisUnProd_mean.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + + newData = data.frame(data.table(UNPROD)[,list(unique=.N, + VH.DEL=num_median(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), + P1=num_median(.SD$P3V.nt.nb, na.rm=T), + N1=num_median(.SD$N1.REGION.nt.nb, na.rm=T), + P2=num_median(.SD$P5D.nt.nb, na.rm=T), + DEL.DH=num_median(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T), + DH.DEL=num_median(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T), + P3=num_median(.SD$P3D.nt.nb, na.rm=T), + N2=num_median(.SD$N2.REGION.nt.nb, na.rm=T), + P4=num_median(.SD$P5J.nt.nb, na.rm=T), + DEL.JH=num_median(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), + Total.Del=num_median(c(.SD$X3V.REGION.trimmed.nt.nb, + .SD$X5D.REGION.trimmed.nt.nb, + .SD$X3D.REGION.trimmed.nt.nb, + .SD$X5J.REGION.trimmed.nt.nb), na.rm=T), + Total.N=num_median( c(.SD$N1.REGION.nt.nb, + .SD$N2.REGION.nt.nb), na.rm=T), + Total.P=num_median(c(.SD$P3V.nt.nb, + .SD$P5D.nt.nb, + .SD$P3D.nt.nb, + .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_median.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) } # ---------------------- AA composition in CDR3 ----------------------