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chr naming fix

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gavinha committed Sep 27, 2018
1 parent a50e6fa commit 9d36ea0127c1d54025dc246c1c540ef981513ca8
Showing with 4 additions and 2 deletions.
  1. +3 −1 code/combineTITAN-ichor.R
  2. +1 −1 code/titanCNA_v1.15.0_TenX.R
@@ -82,7 +82,9 @@ setnames(ichor.cn, c("chr", "start", paste0(id,".copy.number"), paste0(id,".even


## get chromosome style
genomeStyle <- seqlevelsStyle(titan$Chr)
titan$Chromosome <- as.character(titan$Chromosome)
titan.cn$Chr <- as.character(titan.cn$Chr)
genomeStyle <- seqlevelsStyle()[1]
chrs <- c(1:22, "X")
seqlevelsStyle(chrs) <- genomeStyle

@@ -36,7 +36,7 @@ option_list <- list(
make_option(c("--genomeBuild"), type = "character", default = "hg38", help="Genome build to use; will load Seqinfo from GenomeInfoDb."),
make_option(c("--chrs"), type = "character", default = "c(1:22, 'X')", help = "Chromosomes to analyze; string [Default: %default"),
make_option(c("--sex"), type = "character", default = "None", help = "User specified sex: male or female or None [Default: %default]"),
make_option(c("--cytobandFile"), type = "character", default = NULL, help = "Cytoband file should be provided only if reference genome is hg38."),
make_option(c("--cytobandFile"), type = "character", default = "", help = "Cytoband file should be provided only if reference genome is hg38."),
make_option(c("--mapWig"), type = "character", default = NULL, help = "Mappability score file for bin sizes matching cnfile. [Default: %default]"),
make_option(c("--mapThres"), type = "numeric", default = 0.9, help = "Minimum mappability score threshold to use; float [Default: %default]"),
make_option(c("--centromere"), type = "character", default=NULL, help = "Centromere gap file. [Default: %default]"),

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