Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 63:39ea37070e90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Wed, 04 Nov 2015 11:02:01 -0500
parents b1ad6f515338
children 39fff0180d41
comparison
equal deleted inserted replaced
62:b1ad6f515338 63:39ea37070e90
712 patient.fuzzy = patient.fuzzy[!(match.filter.1 | match.filter.3),] 712 patient.fuzzy = patient.fuzzy[!(match.filter.1 | match.filter.3),]
713 713
714 hidden.clone.sequences = c(rows.1[-1,"Clone_Sequence"], rows.3[rows.3$Clone_Sequence != first.clone.sequence,"Clone_Sequence"]) 714 hidden.clone.sequences = c(rows.1[-1,"Clone_Sequence"], rows.3[rows.3$Clone_Sequence != first.clone.sequence,"Clone_Sequence"])
715 merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences) 715 merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)
716 716
717 } else if(nrow(rows.1) > 1){
718 patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),]
719 patient1 = rbind(patient1, sum.1)
720 patient.fuzzy = patient.fuzzy[-match.filter.1,]
717 } else { 721 } else {
718 patient.fuzzy = patient.fuzzy[-1,] 722 patient.fuzzy = patient.fuzzy[-1,]
719 } 723 }
720 724
721 tmp.rows = rbind(rows.1, rows.2, rows.3) 725 tmp.rows = rbind(rows.1, rows.2, rows.3)
743 patientMerge$thresholdValue = pmax(patientMerge[,onx], patientMerge[,ony], patientMerge[,onz]) 747 patientMerge$thresholdValue = pmax(patientMerge[,onx], patientMerge[,ony], patientMerge[,onz])
744 patientMerge12$thresholdValue = pmax(patientMerge12[,onx], patientMerge12[,ony]) 748 patientMerge12$thresholdValue = pmax(patientMerge12[,onx], patientMerge12[,ony])
745 patientMerge13$thresholdValue = pmax(patientMerge13[,onx], patientMerge13[,ony]) 749 patientMerge13$thresholdValue = pmax(patientMerge13[,onx], patientMerge13[,ony])
746 patientMerge23$thresholdValue = pmax(patientMerge23[,onx], patientMerge23[,ony]) 750 patientMerge23$thresholdValue = pmax(patientMerge23[,onx], patientMerge23[,ony])
747 751
748 patient1 = patient1[!(patient1$Clone_Sequence %in% patient.merge.list.second[[label1]]),] 752 patient1 = patient1[!(patient1$Clone_Sequence %in% merge.list[["second"]]),]
749 patient2 = patient2[!(patient2$Clone_Sequence %in% patient.merge.list.second[[label1]]),] 753 patient2 = patient2[!(patient2$Clone_Sequence %in% merge.list[["second"]]),]
750 patient2 = patient3[!(patient3$Clone_Sequence %in% patient.merge.list.second[[label1]]),] 754 patient3 = patient3[!(patient3$Clone_Sequence %in% merge.list[["second"]]),]
751 755
752 if(F){ 756 if(F){
753 patientMerge = merge(patient1, patient2, by="merge") 757 patientMerge = merge(patient1, patient2, by="merge")
754 patientMerge = merge(patientMerge, patient3, by="merge") 758 patientMerge = merge(patientMerge, patient3, by="merge")
755 colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge)))] = paste(colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge), perl=T))], ".z", sep="") 759 colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge)))] = paste(colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge), perl=T))], ".z", sep="")