Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
comparison RScript.r @ 53:8ebe57feecd6 draft
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author | davidvanzessen |
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date | Mon, 12 Oct 2015 10:48:32 -0400 |
parents | c5c2a790d476 |
children | ef5ffc8a6e37 |
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52:c5c2a790d476 | 53:8ebe57feecd6 |
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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 } |