Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 5:9641f3dfc590 draft

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author davidvanzessen
date Mon, 15 Sep 2014 05:38:46 -0400
parents f11df36f43bb
children 8313c6cc65c5
comparison
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4:f11df36f43bb 5:9641f3dfc590
33 dat$paste = paste(dat$Sample, dat$V_Segment_Major_Gene, dat$J_Segment_Major_Gene, dat$CDR3_Sense_Sequence) 33 dat$paste = paste(dat$Sample, dat$V_Segment_Major_Gene, dat$J_Segment_Major_Gene, dat$CDR3_Sense_Sequence)
34 cat("<tr><td>Removing duplicates</td></tr>", file=logfile, append=T) 34 cat("<tr><td>Removing duplicates</td></tr>", file=logfile, append=T)
35 dat = dat[!duplicated(dat$paste),] 35 dat = dat[!duplicated(dat$paste),]
36 patients = split(dat, dat$Patient, drop=T) 36 patients = split(dat, dat$Patient, drop=T)
37 rm(dat) 37 rm(dat)
38 patients = patients[1:5]
39 intervalReads = rev(c(0,10,25,50,100,1000,10000)) 38 intervalReads = rev(c(0,10,25,50,100,1000,10000))
40 intervalFreq = rev(c(0,0.01,0.1,0.5,1,5)) 39 intervalFreq = rev(c(0,0.01,0.1,0.5,1,5))
41 V_Segments = c(".*", "IGHV", "IGHD", "IGKV", "IGKV", "IgKINTR", "TRGV", "TRDV", "TRDD" , "TRBV") 40 V_Segments = c(".*", "IGHV", "IGHD", "IGKV", "IGKV", "IgKINTR", "TRGV", "TRDV", "TRDD" , "TRBV")
42 J_Segments = c(".*", ".*", ".*", "IGKJ", "KDE", ".*", ".*", ".*", ".*", ".*") 41 J_Segments = c(".*", ".*", ".*", "IGKJ", "KDE", ".*", ".*", ".*", ".*", ".*")
43 Titles = c("Total", "IGH-Vh-Jh", "IGH-Dh-Jh", "Vk-Jk", "Vk-Kde" , "Intron-Kde", "TCRG", "TCRD-Vd-Dd", "TCRD-Dd-Dd", "TCRB-Vb-Jb") 42 Titles = c("Total", "IGH-Vh-Jh", "IGH-Dh-Jh", "Vk-Jk", "Vk-Kde" , "Intron-Kde", "TCRG", "TCRD-Vd-Dd", "TCRD-Dd-Dd", "TCRB-Vb-Jb")