Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 64:39fff0180d41 draft

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author davidvanzessen
date Thu, 05 Nov 2015 09:07:03 -0500
parents 39ea37070e90
children 7a63e90cfc3d
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63:39ea37070e90 64:39fff0180d41
616 CDR3_Sense_Sequence = rows.1[1,"CDR3_Sense_Sequence"], 616 CDR3_Sense_Sequence = rows.1[1,"CDR3_Sense_Sequence"],
617 Related_to_leukemia_clone = F, 617 Related_to_leukemia_clone = F,
618 Frequency = sum(rows.1$Frequency), 618 Frequency = sum(rows.1$Frequency),
619 locus_V = rows.1[1,"locus_V"], 619 locus_V = rows.1[1,"locus_V"],
620 locus_J = rows.1[1,"locus_J"], 620 locus_J = rows.1[1,"locus_J"],
621 uniqueID = rows.1[1,"uniqueID"],
621 normalized_read_count = sum(rows.1$normalized_read_count)) 622 normalized_read_count = sum(rows.1$normalized_read_count))
622 sum.2 = sum.1[NULL,] 623 sum.2 = sum.1[NULL,]
623 rows.2 = patient.fuzzy[match.filter.2,] 624 rows.2 = patient.fuzzy[match.filter.2,]
624 if(matches.in.2){ 625 if(matches.in.2){
625 sum.2 = data.frame(merge = first.clone.sequence, 626 sum.2 = data.frame(merge = first.clone.sequence,
637 CDR3_Sense_Sequence = rows.2[1,"CDR3_Sense_Sequence"], 638 CDR3_Sense_Sequence = rows.2[1,"CDR3_Sense_Sequence"],
638 Related_to_leukemia_clone = F, 639 Related_to_leukemia_clone = F,
639 Frequency = sum(rows.2$Frequency), 640 Frequency = sum(rows.2$Frequency),
640 locus_V = rows.2[1,"locus_V"], 641 locus_V = rows.2[1,"locus_V"],
641 locus_J = rows.2[1,"locus_J"], 642 locus_J = rows.2[1,"locus_J"],
643 uniqueID = rows.2[1,"uniqueID"],
642 normalized_read_count = sum(rows.2$normalized_read_count)) 644 normalized_read_count = sum(rows.2$normalized_read_count))
643 } 645 }
644 646
645 sum.3 = sum.1[NULL,] 647 sum.3 = sum.1[NULL,]
646 rows.3 = patient.fuzzy[match.filter.3,] 648 rows.3 = patient.fuzzy[match.filter.3,]
660 CDR3_Sense_Sequence = rows.3[1,"CDR3_Sense_Sequence"], 662 CDR3_Sense_Sequence = rows.3[1,"CDR3_Sense_Sequence"],
661 Related_to_leukemia_clone = F, 663 Related_to_leukemia_clone = F,
662 Frequency = sum(rows.3$Frequency), 664 Frequency = sum(rows.3$Frequency),
663 locus_V = rows.3[1,"locus_V"], 665 locus_V = rows.3[1,"locus_V"],
664 locus_J = rows.3[1,"locus_J"], 666 locus_J = rows.3[1,"locus_J"],
667 uniqueID = rows.3[1,"uniqueID"],
665 normalized_read_count = sum(rows.3$normalized_read_count)) 668 normalized_read_count = sum(rows.3$normalized_read_count))
666 } 669 }
667 670
668 if(matches.in.2 & matches.in.3){ 671 if(matches.in.2 & matches.in.3){
669 merge.123 = merge(sum.1, sum.2, by="merge") 672 merge.123 = merge(sum.1, sum.2, by="merge")
714 hidden.clone.sequences = c(rows.1[-1,"Clone_Sequence"], rows.3[rows.3$Clone_Sequence != first.clone.sequence,"Clone_Sequence"]) 717 hidden.clone.sequences = c(rows.1[-1,"Clone_Sequence"], rows.3[rows.3$Clone_Sequence != first.clone.sequence,"Clone_Sequence"])
715 merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences) 718 merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)
716 719
717 } else if(nrow(rows.1) > 1){ 720 } else if(nrow(rows.1) > 1){
718 patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),] 721 patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),]
719 patient1 = rbind(patient1, sum.1) 722 print(names(patient1)[names(patient1) %in% sum.1])
723 print(names(patient1)[!(names(patient1) %in% sum.1)])
724 print(names(patient1))
725 print(names(sum.1))
726 print(summary(sum.1))
727 print(summary(patient1))
728 print(dim(sum.1))
729 print(dim(patient1))
730 print(head(sum.1[,names(patient1)]))
731 patient1 = rbind(patient1, sum.1[,names(patient1)])
720 patient.fuzzy = patient.fuzzy[-match.filter.1,] 732 patient.fuzzy = patient.fuzzy[-match.filter.1,]
721 } else { 733 } else {
722 patient.fuzzy = patient.fuzzy[-1,] 734 patient.fuzzy = patient.fuzzy[-1,]
723 } 735 }
724 736