Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/RScript.r @ 13:d3ebaa2d2fe0 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 20 Dec 2016 06:02:44 -0500 |
| parents | efa1f5a17b6e |
| children | 15961ca8d9ce |
line wrap: on
line diff
--- a/report_clonality/RScript.r Mon Dec 19 10:03:41 2016 -0500 +++ b/report_clonality/RScript.r Tue Dec 20 06:02:44 2016 -0500 @@ -47,7 +47,7 @@ print("Report Clonality - Data preperation") -inputdata = read.table(infile, sep="\t", header=TRUE, fill=T, comment.char="") +inputdata = read.table(infile, sep="\t", header=TRUE, fill=T, comment.char="", stringsAsFactors=F) print(paste("nrows: ", nrow(inputdata))) @@ -92,6 +92,12 @@ } } +for(i in 1:nrow(UNPROD)){ + if(!is.numeric(UNPROD[i,"CDR3.Length"])){ + UNPROD[i,"CDR3.Length"] = 0 + } +} + prod.sample.count = data.frame(data.table(PRODF)[, list(Productive=.N), by=c("Sample")]) prod.rep.count = data.frame(data.table(PRODF)[, list(Productive=.N), by=c("Sample", "Replicate")]) @@ -591,7 +597,7 @@ res[is.na(res)] = 0 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) - print(infer.result) + #print(infer.result) write.table(data.table(infer.result[[12]]), file=paste("lymphclon_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) @@ -734,7 +740,7 @@ Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), - Median.CDR3.l=median(.SD$CDR3.Length)), + Median.CDR3.l=as.double(median(.SD$CDR3.Length))), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) write.table(newData, "junctionAnalysisProd_mean.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) @@ -753,7 +759,7 @@ Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), - Median.CDR3.l=median(.SD$CDR3.Length)), + Median.CDR3.l=as.double(median(.SD$CDR3.Length))), 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) @@ -772,7 +778,7 @@ Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), - Median.CDR3.l=median(.SD$CDR3.Length)), + Median.CDR3.l=as.double(median(.SD$CDR3.Length))), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) write.table(newData, "junctionAnalysisUnProd_mean.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) @@ -791,7 +797,7 @@ Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), - Median.CDR3.l=median(.SD$CDR3.Length)), + Median.CDR3.l=as.double(median(.SD$CDR3.Length))), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)