Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 53:8ebe57feecd6 draft

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author davidvanzessen
date Mon, 12 Oct 2015 10:48:32 -0400
parents c5c2a790d476
children ef5ffc8a6e37
comparison
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52:c5c2a790d476 53:8ebe57feecd6
724 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 724 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
725 725
726 one = triplets[triplets$Sample == "14696_reg_BM",] 726 one = triplets[triplets$Sample == "14696_reg_BM",]
727 two = triplets[triplets$Sample == "24536_reg_BM",] 727 two = triplets[triplets$Sample == "24536_reg_BM",]
728 three = triplets[triplets$Sample == "24062_reg_BM",] 728 three = triplets[triplets$Sample == "24062_reg_BM",]
729 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count", T) 729 tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="normalized_read_count", T)
730 730
731 one = triplets[triplets$Sample == "16278_Left",] 731 one = triplets[triplets$Sample == "16278_Left",]
732 two = triplets[triplets$Sample == "26402_Left",] 732 two = triplets[triplets$Sample == "26402_Left",]
733 three = triplets[triplets$Sample == "26759_Left",] 733 three = triplets[triplets$Sample == "26759_Left",]
734 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count", T) 734 tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="normalized_read_count", T)
735 735
736 one = triplets[triplets$Sample == "16278_Right",] 736 one = triplets[triplets$Sample == "16278_Right",]
737 two = triplets[triplets$Sample == "26402_Right",] 737 two = triplets[triplets$Sample == "26402_Right",]
738 three = triplets[triplets$Sample == "26759_Right",] 738 three = triplets[triplets$Sample == "26759_Right",]
739 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count", T) 739 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="normalized_read_count", T)
740 740
741 741
742 interval = intervalFreq 742 interval = intervalFreq
743 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval)) 743 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
744 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 744 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
745 745
746 one = triplets[triplets$Sample == "14696_reg_BM",] 746 one = triplets[triplets$Sample == "14696_reg_BM",]
747 two = triplets[triplets$Sample == "24536_reg_BM",] 747 two = triplets[triplets$Sample == "24536_reg_BM",]
748 three = triplets[triplets$Sample == "24062_reg_BM",] 748 three = triplets[triplets$Sample == "24062_reg_BM",]
749 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", F) 749 tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="Frequency", F)
750 750
751 one = triplets[triplets$Sample == "16278_Left",] 751 one = triplets[triplets$Sample == "16278_Left",]
752 two = triplets[triplets$Sample == "26402_Left",] 752 two = triplets[triplets$Sample == "26402_Left",]
753 three = triplets[triplets$Sample == "26759_Left",] 753 three = triplets[triplets$Sample == "26759_Left",]
754 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", F) 754 tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="Frequency", F)
755 755
756 one = triplets[triplets$Sample == "16278_Right",] 756 one = triplets[triplets$Sample == "16278_Right",]
757 two = triplets[triplets$Sample == "26402_Right",] 757 two = triplets[triplets$Sample == "26402_Right",]
758 three = triplets[triplets$Sample == "26759_Right",] 758 three = triplets[triplets$Sample == "26759_Right",]
759 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", F) 759 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="Frequency", F)
760 } else { 760 } else {
761 cat("", file="triplets.txt") 761 cat("", file="triplets.txt")
762 } 762 }