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adding line in procSnps() to ensure required field order #194

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adding line in procSnps() to ensure required field order #194

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2 changes: 2 additions & 0 deletions R/facets-procreads.R
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Expand Up @@ -12,6 +12,8 @@ procSnps <- function(rcmat, ndepth=35, het.thresh=0.25, snp.nbhd=250, nX=23, unm
row.names(rcmat) <- NULL # reset row names so that it's 1:nsnps
rcmat$NOR.RD = 1 - rcmat$NOR.RD/rcmat$NOR.DP
rcmat$TUM.RD = 1 - rcmat$TUM.RD/rcmat$TUM.DP
# ensure rcmat fields in required order
rcmat <- rcmat[,c('Chromosome','Position','NOR.DP','NOR.RD','TUM.DP','TUM.RD')]
names(rcmat) = c("chrom", "maploc", "rCountN", "vafN", "rCountT", "vafT")
# make chromosome ordered and numeric
rcmat$chrom <- as.numeric(ordered(rcmat$chrom, levels = chromlevels))
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