Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 15:d137974763b3 draft

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author davidvanzessen
date Thu, 05 Feb 2015 07:57:21 -0500
parents 1735e91a8f4b
children 7a9debac9a97
comparison
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14:1735e91a8f4b 15:d137974763b3
18 dat = read.table(inFile, header=T, sep="\t", dec=".", fill=T, stringsAsFactors=F) 18 dat = read.table(inFile, header=T, sep="\t", dec=".", fill=T, stringsAsFactors=F)
19 dat = dat[!is.na(dat$Patient),] 19 dat = dat[!is.na(dat$Patient),]
20 dat$Related_to_leukemia_clone = F 20 dat$Related_to_leukemia_clone = F
21 21
22 setwd(outDir) 22 setwd(outDir)
23 write(paste("TMP='", outDir, "'"), file=file.path(Sys.getenv('R_USER'), '.Renviron'))
23 cat("<tr><td>Selecting first V/J Genes</td></tr>", file=logfile, append=T) 24 cat("<tr><td>Selecting first V/J Genes</td></tr>", file=logfile, append=T)
24 dat$V_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$V_Segment_Major_Gene), "; "), "[[", 1))) 25 dat$V_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$V_Segment_Major_Gene), "; "), "[[", 1)))
25 dat$J_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$J_Segment_Major_Gene), "; "), "[[", 1))) 26 dat$J_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$J_Segment_Major_Gene), "; "), "[[", 1)))
26 27
27 cat("<tr><td>Calculating Frequency</td></tr>", file=logfile, append=T) 28 cat("<tr><td>Calculating Frequency</td></tr>", file=logfile, append=T)
121 for(iter in 1:length(product[,1])){ 122 for(iter in 1:length(product[,1])){
122 threshhold = product[iter,threshholdIndex] 123 threshhold = product[iter,threshholdIndex]
123 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="") 124 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
124 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="") 125 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
125 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) 126 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)
126 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)) 127 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[both,]$Clone_Sequence.x))
127 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)) 128 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[both,]$Clone_Sequence.x))
128 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count)) 129 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count))
129 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count)) 130 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count))
130 res1 = append(res1, sum(one)) 131 res1 = append(res1, sum(one))
131 res2 = append(res2, sum(two)) 132 res2 = append(res2, sum(two))
132 resBoth = append(resBoth, sum(both)) 133 resBoth = append(resBoth, sum(both))
133 locussum1 = append(locussum1, sum(patient1[(grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene)),]$normalized_read_count)) 134 locussum1 = append(locussum1, sum(patient1[(grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene)),]$normalized_read_count))
134 locussum2 = append(locussum2, sum(patient2[(grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene)),]$normalized_read_count)) 135 locussum2 = append(locussum2, sum(patient2[(grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene)),]$normalized_read_count))
135 #threshhold = 0 136 #threshhold = 0
136 if(threshhold != 0){ 137 if(threshhold != 0){
137 if(sum(one) > 0){ 138 if(sum(one) > 0){
138 dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "CDR3_Sense_Sequence", "Related_to_leukemia_clone")] 139 dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
139 colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "CDR3 Sequence", "Related_to_leukemia_clone") 140 colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Clone Sequence", "Related_to_leukemia_clone")
140 filenameOne = paste(oneSample, "_", product[iter, titleIndex], "_", threshhold, sep="") 141 filenameOne = paste(oneSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
141 write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 142 write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
142 } 143 }
143 if(sum(two) > 0){ 144 if(sum(two) > 0){
144 dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "CDR3_Sense_Sequence", "Related_to_leukemia_clone")] 145 dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
145 colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "CDR3 Sequence", "Related_to_leukemia_clone") 146 colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Clone Sequence", "Related_to_leukemia_clone")
146 filenameTwo = paste(twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="") 147 filenameTwo = paste(twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
147 write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 148 write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
148 } 149 }
149 } 150 }
150 if(sum(both) > 0){ 151 if(sum(both) > 0){
151 dfBoth = patientMerge[both,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "CDR3_Sense_Sequence.x", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y")] 152 dfBoth = patientMerge[both,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "Clone_Sequence.x", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y")]
152 colnames(dfBoth) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"CDR3 Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample)) 153 colnames(dfBoth) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"Clone Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample))
153 filenameBoth = paste(oneSample, "_", twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="") 154 filenameBoth = paste(oneSample, "_", twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
154 write.table(dfBoth, file=paste(filenameBoth, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 155 write.table(dfBoth, file=paste(filenameBoth, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
155 } 156 }
156 } 157 }
157 patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "Both"=resBoth, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "Sum"=res1 + res2 + resBoth, "percentage" = round((resBoth/(res1 + res2 + resBoth)) * 100, digits=2), "Locus_sum1"=locussum1, "Locus_sum2"=locussum2) 158 patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "Both"=resBoth, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "Sum"=res1 + res2 + resBoth, "percentage" = round((resBoth/(res1 + res2 + resBoth)) * 100, digits=2), "Locus_sum1"=locussum1, "Locus_sum2"=locussum2)
240 241
241 #patient1$merge = paste(patient1$V_Segment_Major_Gene, patient1$J_Segment_Major_Gene, patient1$CDR3_Sense_Sequence) 242 #patient1$merge = paste(patient1$V_Segment_Major_Gene, patient1$J_Segment_Major_Gene, patient1$CDR3_Sense_Sequence)
242 #patient2$merge = paste(patient2$V_Segment_Major_Gene, patient2$J_Segment_Major_Gene, patient2$CDR3_Sense_Sequence) 243 #patient2$merge = paste(patient2$V_Segment_Major_Gene, patient2$J_Segment_Major_Gene, patient2$CDR3_Sense_Sequence)
243 #patient3$merge = paste(patient3$V_Segment_Major_Gene, patient3$J_Segment_Major_Gene, patient3$CDR3_Sense_Sequence) 244 #patient3$merge = paste(patient3$V_Segment_Major_Gene, patient3$J_Segment_Major_Gene, patient3$CDR3_Sense_Sequence)
244 245
245 patient1$merge = paste(patient1$CDR3_Sense_Sequence) 246 patient1$merge = paste(patient1$Clone_Sequence)
246 patient2$merge = paste(patient2$CDR3_Sense_Sequence) 247 patient2$merge = paste(patient2$Clone_Sequence)
247 patient3$merge = paste(patient3$CDR3_Sense_Sequence) 248 patient3$merge = paste(patient3$Clone_Sequence)
248 249
249 patientMerge = merge(patient1, patient2, by="merge") 250 patientMerge = merge(patient1, patient2, by="merge")
250 patientMerge = merge(patientMerge, patient3, by="merge") 251 patientMerge = merge(patientMerge, patient3, by="merge")
251 colnames(patientMerge)[30:length(colnames(patientMerge))] = paste(colnames(patientMerge)[30:length(colnames(patientMerge))], ".z", sep="") 252 colnames(patientMerge)[30:length(colnames(patientMerge))] = paste(colnames(patientMerge)[30:length(colnames(patientMerge))], ".z", sep="")
252 res1 = vector() 253 res1 = vector()
263 for(iter in 1:length(product[,1])){ 264 for(iter in 1:length(product[,1])){
264 threshhold = product[iter,threshholdIndex] 265 threshhold = product[iter,threshholdIndex]
265 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="") 266 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
266 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="") 267 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
267 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) 268 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)
268 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)) 269 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x))
269 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)) 270 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x))
270 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)) 271 three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x))
271 272
272 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count)) 273 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count))
273 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count)) 274 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count))
274 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count)) 275 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count))
275 res1 = append(res1, sum(one)) 276 res1 = append(res1, sum(one))
277 res3 = append(res3, sum(three)) 278 res3 = append(res3, sum(three))
278 resAll = append(resAll, sum(all)) 279 resAll = append(resAll, sum(all))
279 #threshhold = 0 280 #threshhold = 0
280 if(threshhold != 0){ 281 if(threshhold != 0){
281 if(sum(one) > 0){ 282 if(sum(one) > 0){
282 dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "CDR3_Sense_Sequence", "Related_to_leukemia_clone")] 283 dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
283 colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone") 284 colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Clone Sequence", "Related_to_leukemia_clone")
284 filenameOne = paste(label1, "_", product[iter, titleIndex], "_", threshhold, sep="") 285 filenameOne = paste(label1, "_", product[iter, titleIndex], "_", threshhold, sep="")
285 write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 286 write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
286 } 287 }
287 if(sum(two) > 0){ 288 if(sum(two) > 0){
288 dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "CDR3_Sense_Sequence", "Related_to_leukemia_clone")] 289 dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
289 colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone") 290 colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Clone Sequence", "Related_to_leukemia_clone")
290 filenameTwo = paste(label2, "_", product[iter, titleIndex], "_", threshhold, sep="") 291 filenameTwo = paste(label2, "_", product[iter, titleIndex], "_", threshhold, sep="")
291 write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 292 write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
292 } 293 }
293 if(sum(three) > 0){ 294 if(sum(three) > 0){
294 dfThree = patient3[three,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "CDR3_Sense_Sequence", "Related_to_leukemia_clone")] 295 dfThree = patient3[three,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
295 colnames(dfThree) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone") 296 colnames(dfThree) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Clone Sequence", "Related_to_leukemia_clone")
296 filenameThree = paste(label3, "_", product[iter, titleIndex], "_", threshhold, sep="") 297 filenameThree = paste(label3, "_", product[iter, titleIndex], "_", threshhold, sep="")
297 write.table(dfThree, file=paste(filenameThree, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 298 write.table(dfThree, file=paste(filenameThree, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
298 } 299 }
299 } 300 }
300 if(sum(all) > 0){ 301 if(sum(all) > 0){
301 dfAll = patientMerge[all,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "CDR3_Sense_Sequence.x", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y", "V_Segment_Major_Gene.z", "J_Segment_Major_Gene.z", "normalized_read_count.z", "Frequency.z", "Related_to_leukemia_clone.z")] 302 dfAll = patientMerge[all,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "Clone_Sequence.x", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y", "V_Segment_Major_Gene.z", "J_Segment_Major_Gene.z", "normalized_read_count.z", "Frequency.z", "Related_to_leukemia_clone.z")]
302 colnames(dfAll) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"CDR3_Sense_Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample), paste("Proximal segment", threeSample), paste("Distal segment", threeSample), paste("Normalized_Read_Count", threeSample), paste("Frequency", threeSample), paste("Related_to_leukemia_clone", threeSample)) 303 colnames(dfAll) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"Clone Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample), paste("Proximal segment", threeSample), paste("Distal segment", threeSample), paste("Normalized_Read_Count", threeSample), paste("Frequency", threeSample), paste("Related_to_leukemia_clone", threeSample))
303 filenameAll = paste(label1, "_", label2, "_", label3, "_", product[iter, titleIndex], "_", threshhold, sep="") 304 filenameAll = paste(label1, "_", label2, "_", label3, "_", product[iter, titleIndex], "_", threshhold, sep="")
304 write.table(dfAll, file=paste(filenameAll, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 305 write.table(dfAll, file=paste(filenameAll, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
305 } 306 }
306 } 307 }
307 patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "All"=resAll, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "tmp3"=res3, "read_count3"=round(read3Count)) 308 patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "All"=resAll, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "tmp3"=res3, "read_count3"=round(read3Count))