Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 66:ef3ac4f431bb draft

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Uploaded
author davidvanzessen
date Fri, 20 Nov 2015 08:27:13 -0500
parents 7a63e90cfc3d
children 40c72b9ffc79
comparison
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65:7a63e90cfc3d 66:ef3ac4f431bb
15 library(grid) 15 library(grid)
16 library(parallel) 16 library(parallel)
17 #require(xtable) 17 #require(xtable)
18 cat("<tr><td>Reading input</td></tr>", file=logfile, append=T) 18 cat("<tr><td>Reading input</td></tr>", file=logfile, append=T)
19 dat = read.table(inFile, header=T, sep="\t", dec=".", fill=T, stringsAsFactors=F) 19 dat = read.table(inFile, header=T, sep="\t", dec=".", fill=T, stringsAsFactors=F)
20 dat = dat[,c("Patient", "Receptor", "Sample", "Cell_Count", "Clone_Molecule_Count_From_Spikes", "Log10_Frequency", "Total_Read_Count", "J_Segment_Major_Gene", "V_Segment_Major_Gene", "CDR3_Sense_Sequence", "Related_to_leukemia_clone", "Clone_Sequence")] 20 dat = dat[,c("Patient", "Receptor", "Sample", "Cell_Count", "Clone_Molecule_Count_From_Spikes", "Log10_Frequency", "Total_Read_Count", "J_Segment_Major_Gene", "V_Segment_Major_Gene", "CDR3_Sense_Sequence", "Clone_Sequence")]
21 dat$dsPerM = 0 21 dat$dsPerM = 0
22 dat = dat[!is.na(dat$Patient),] 22 dat = dat[!is.na(dat$Patient),]
23 dat$Related_to_leukemia_clone = F 23 dat$Related_to_leukemia_clone = F
24 24
25 setwd(outDir) 25 setwd(outDir)