Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 16:cf1def1aaa74 draft

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author davidvanzessen
date Fri, 06 Nov 2015 05:12:17 -0500
parents b45a74248628
children ee1bda8c27c8
comparison
equal deleted inserted replaced
15:6e068ef43336 16:cf1def1aaa74
561 } 561 }
562 562
563 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") 563 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")
564 if(all(imgtcolumns %in% colnames(inputdata))) 564 if(all(imgtcolumns %in% colnames(inputdata)))
565 { 565 {
566 print("MEAN P3V.nt.nb:")
567 print(PRODF$P3V.nt.nb)
568 print(mean(PRODF$P3V.nt.nb, na.rm=T))
569 print(head(PRODF))
570 newData = data.frame(data.table(PRODF)[,list(unique=.N, 566 newData = data.frame(data.table(PRODF)[,list(unique=.N,
571 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), 567 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
572 P1=mean(.SD$P3V.nt.nb, na.rm=T), 568 P1=mean(.SD$P3V.nt.nb, na.rm=T),
573 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T), 569 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T),
574 P2=mean(.SD$P5D.nt.nb, na.rm=T), 570 P2=mean(.SD$P5D.nt.nb, na.rm=T),
589 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + 585 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) +
590 mean(.SD$P5D.nt.nb, na.rm=T) + 586 mean(.SD$P5D.nt.nb, na.rm=T) +
591 mean(.SD$P3D.nt.nb, na.rm=T) + 587 mean(.SD$P3D.nt.nb, na.rm=T) +
592 mean(.SD$P5J.nt.nb, na.rm=T))), 588 mean(.SD$P5J.nt.nb, na.rm=T))),
593 by=c("Sample")]) 589 by=c("Sample")])
590 print(newData)
591 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
594 write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) 592 write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
595 593
596 newData = data.frame(data.table(UNPROD)[,list(unique=.N, 594 newData = data.frame(data.table(UNPROD)[,list(unique=.N,
597 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), 595 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
598 P1=mean(.SD$P3V.nt.nb, na.rm=T), 596 P1=mean(.SD$P3V.nt.nb, na.rm=T),
615 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + 613 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) +
616 mean(.SD$P5D.nt.nb, na.rm=T) + 614 mean(.SD$P5D.nt.nb, na.rm=T) +
617 mean(.SD$P3D.nt.nb, na.rm=T) + 615 mean(.SD$P3D.nt.nb, na.rm=T) +
618 mean(.SD$P5J.nt.nb, na.rm=T))), 616 mean(.SD$P5J.nt.nb, na.rm=T))),
619 by=c("Sample")]) 617 by=c("Sample")])
618 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
620 write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) 619 write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
621 } 620 }
622 621
623 # ---------------------- AA composition in CDR3 ---------------------- 622 # ---------------------- AA composition in CDR3 ----------------------
624 623