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genomestyle for centromere and targetedSequences

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gavinha committed Aug 3, 2018
1 parent 7ff2ea9 commit dae6562fd9adf7726444b6fb13283d1da878e453
Showing with 2 additions and 0 deletions.
  1. +2 −0 R/haplotype.R
@@ -53,10 +53,12 @@ loadReadCountsFromBed <- function(counts, chrs = c(1:22, "X", "Y"), gc = NULL, m
# remove centromeres
if (!is.null(centromere)){
centromere$Chr <- setGenomeStyle(centromere$Chr, genomeStyle)
counts <- excludeCentromere(counts, centromere, flankLength = flankLength)
}
# keep targeted sequences
if (!is.null(targetedSequences)){
targetedSequences[,1] <- setGenomeStyle(targetedSequences[,1], genomeStyle)
countsExons <- filterByTargetedSequences(counts, targetedSequences)
counts <- counts[countsExons$ix,]
}

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