Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 17:7a9debac9a97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 05 Feb 2015 08:22:19 -0500
parents d137974763b3
children f23d3be6fbc8
comparison
equal deleted inserted replaced
16:95c9d82b3cd4 17:7a9debac9a97
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'))
24 cat("<tr><td>Selecting first V/J Genes</td></tr>", file=logfile, append=T) 23 cat("<tr><td>Selecting first V/J Genes</td></tr>", file=logfile, append=T)
25 dat$V_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$V_Segment_Major_Gene), "; "), "[[", 1))) 24 dat$V_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$V_Segment_Major_Gene), "; "), "[[", 1)))
26 dat$J_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$J_Segment_Major_Gene), "; "), "[[", 1))) 25 dat$J_Segment_Major_Gene = as.factor(as.character(lapply(strsplit(as.character(dat$J_Segment_Major_Gene), "; "), "[[", 1)))
27 26
28 cat("<tr><td>Calculating Frequency</td></tr>", file=logfile, append=T) 27 cat("<tr><td>Calculating Frequency</td></tr>", file=logfile, append=T)