Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 10:974febc99fd4 draft

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Uploaded
author davidvanzessen
date Wed, 01 Oct 2014 08:11:47 -0400
parents 58a28427930e
children bc4612998d50
comparison
equal deleted inserted replaced
9:58a28427930e 10:974febc99fd4
105 for(iter in 1:length(product[,1])){ 105 for(iter in 1:length(product[,1])){
106 threshhold = product[iter,threshholdIndex] 106 threshhold = product[iter,threshholdIndex]
107 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="") 107 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
108 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="") 108 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
109 both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold) 109 both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold)
110 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence)) 110 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence.x))
111 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence)) 111 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence.x))
112 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.x)) 112 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.x))
113 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.y)) 113 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.y))
114 res1 = append(res1, sum(one)) 114 res1 = append(res1, sum(one))
115 res2 = append(res2, sum(two)) 115 res2 = append(res2, sum(two))
116 resBoth = append(resBoth, sum(both)) 116 resBoth = append(resBoth, sum(both))
242 for(iter in 1:length(product[,1])){ 242 for(iter in 1:length(product[,1])){
243 threshhold = product[iter,threshholdIndex] 243 threshhold = product[iter,threshholdIndex]
244 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="") 244 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
245 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="") 245 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
246 all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold & patientMerge[,paste(on, ".z", sep="")] > threshhold) 246 all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold & patientMerge[,paste(on, ".z", sep="")] > threshhold)
247 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence)) 247 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence.x))
248 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence)) 248 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence.x))
249 three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence)) 249 three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence.x))
250 250
251 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x)) 251 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
252 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y)) 252 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
253 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z)) 253 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z))
254 res1 = append(res1, sum(one)) 254 res1 = append(res1, sum(one))