Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/RScript.r @ 3:beaa487ecf43 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 07 Dec 2016 08:36:23 -0500 |
| parents | 90a05ff900db |
| children |
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--- a/report_clonality/RScript.r Mon Sep 05 11:15:22 2016 -0400 +++ b/report_clonality/RScript.r Wed Dec 07 08:36:23 2016 -0500 @@ -10,7 +10,7 @@ library(ggplot2) if (!("plyr" %in% rownames(installed.packages()))) { install.packages("plyr", repos="http://cran.xl-mirror.nl/") -} +} library(plyr) if (!("data.table" %in% rownames(installed.packages()))) { @@ -717,7 +717,8 @@ DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), - Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T))), + Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), + Median.CDR3.l=median(.SD$CDR3.Length.DNA)), 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) @@ -735,7 +736,8 @@ DEL.JH=num_median(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), - Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T))), + Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), + Median.CDR3.l=median(.SD$CDR3.Length.DNA)), 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) @@ -753,7 +755,8 @@ DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), - Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T))), + Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), + Median.CDR3.l=median(.SD$CDR3.Length.DNA)), 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) @@ -771,7 +774,8 @@ DEL.JH=num_median(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)), Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)), - Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T))), + Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)), + Median.CDR3.l=median(.SD$CDR3.Length.DNA)), by=c("Sample")]) newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)