Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 17:ee1bda8c27c8 draft

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author davidvanzessen
date Mon, 09 Nov 2015 08:28:31 -0500
parents cf1def1aaa74
children 431797cd74c8
comparison
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16:cf1def1aaa74 17:ee1bda8c27c8
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("found IMGT columns, running junction analysis")
566 newData = data.frame(data.table(PRODF)[,list(unique=.N, 567 newData = data.frame(data.table(PRODF)[,list(unique=.N,
567 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), 568 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
568 P1=mean(.SD$P3V.nt.nb, na.rm=T), 569 P1=mean(.SD$P3V.nt.nb, na.rm=T),
569 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T), 570 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T),
570 P2=mean(.SD$P5D.nt.nb, na.rm=T), 571 P2=mean(.SD$P5D.nt.nb, na.rm=T),
585 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + 586 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) +
586 mean(.SD$P5D.nt.nb, na.rm=T) + 587 mean(.SD$P5D.nt.nb, na.rm=T) +
587 mean(.SD$P3D.nt.nb, na.rm=T) + 588 mean(.SD$P3D.nt.nb, na.rm=T) +
588 mean(.SD$P5J.nt.nb, na.rm=T))), 589 mean(.SD$P5J.nt.nb, na.rm=T))),
589 by=c("Sample")]) 590 by=c("Sample")])
590 print(newData)
591 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) 591 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
592 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)
593 593
594 newData = data.frame(data.table(UNPROD)[,list(unique=.N, 594 newData = data.frame(data.table(UNPROD)[,list(unique=.N,
595 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),
600 DH.DEL=mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T), 600 DH.DEL=mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T),
601 P3=mean(.SD$P3D.nt.nb, na.rm=T), 601 P3=mean(.SD$P3D.nt.nb, na.rm=T),
602 N2=mean(.SD$N2.REGION.nt.nb, na.rm=T), 602 N2=mean(.SD$N2.REGION.nt.nb, na.rm=T),
603 P4=mean(.SD$P5J.nt.nb, na.rm=T), 603 P4=mean(.SD$P5J.nt.nb, na.rm=T),
604 DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), 604 DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T),
605 Total.Del=( mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + 605 Total.Del=(mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) +
606 mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + 606 mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) +
607 mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) + 607 mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) +
608 mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)), 608 mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)),
609 609 Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) +
610 Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) + 610 mean(.SD$N2.REGION.nt.nb, na.rm=T)),
611 mean(.SD$N2.REGION.nt.nb, na.rm=T)), 611 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) +
612 612 mean(.SD$P5D.nt.nb, na.rm=T) +
613 Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + 613 mean(.SD$P3D.nt.nb, na.rm=T) +
614 mean(.SD$P5D.nt.nb, na.rm=T) + 614 mean(.SD$P5J.nt.nb, na.rm=T))),
615 mean(.SD$P3D.nt.nb, na.rm=T) +
616 mean(.SD$P5J.nt.nb, na.rm=T))),
617 by=c("Sample")]) 615 by=c("Sample")])
618 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1) 616 newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
619 write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) 617 write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
620 } 618 }
621 619