Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 19:672d5e010b1f draft

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author davidvanzessen
date Fri, 25 Dec 2015 05:35:06 -0500
parents 431797cd74c8
children f2010de70741
comparison
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18:431797cd74c8 19:672d5e010b1f
582 582
583 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") 583 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")
584 if(all(imgtcolumns %in% colnames(inputdata))) 584 if(all(imgtcolumns %in% colnames(inputdata)))
585 { 585 {
586 print("found IMGT columns, running junction analysis") 586 print("found IMGT columns, running junction analysis")
587
588 if(locus %in% c("IGK","IGL", "TRA", "TRG")){
589 print("VJ recombination, using N column for junction analysis")
590 print(names(PRODF))
591 print(head(PRODF$N.REGION.nt.nb, 30))
592 PRODF$N1.REGION.nt.nb = PRODF$N.REGION.nt.nb
593 }
594
587 newData = data.frame(data.table(PRODF)[,list(unique=.N, 595 newData = data.frame(data.table(PRODF)[,list(unique=.N,
588 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), 596 VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
589 P1=mean(.SD$P3V.nt.nb, na.rm=T), 597 P1=mean(.SD$P3V.nt.nb, na.rm=T),
590 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T), 598 N1=mean(.SD$N1.REGION.nt.nb, na.rm=T),
591 P2=mean(.SD$P5D.nt.nb, na.rm=T), 599 P2=mean(.SD$P5D.nt.nb, na.rm=T),