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hg38 plots: data frame fix for cytoband

The fixes for genes and cytoband chromosome naming (8fb529d)
changed the conversion of the cytoband object into a data frame, which
causes plotIdiogram.hg38 to be unhappy:
Error in ESC[38;5;5m[.data.tableESC[0m(cytoband, cytoband[, "chrom"] == chromosome, ) :
  i is invalid type (matrix). Perhaps in future a 2 column matrix could return a list of elements of DT (in the spirit of A[B] in FAQ 2.14). Please report to data.table issue tracker if you'd like this, or add your comments to FR #657.
Calls: plotIdiogram.hg38 -> [ -> [.data.table
This adds the conversion back in after the chromosome handling.
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chapmanb committed Nov 12, 2018
1 parent 8d0c38d commit 5e029de933dc62209d577ca83426333cc899fbd6
Showing with 1 addition and 0 deletions.
  1. +1 −0 scripts/R_scripts/titanCNA.R
@@ -294,6 +294,7 @@ if (genomeBuild == "hg38" && file.exists(cytobandFile)){
names(cytoband) <- c("chrom", "start", "end", "name", "gieStain")
cytoband <- cytoband[chrom %in% chrs]
cytoband$chrom <- setGenomeStyle(cytoband$chrom, genomeStyle = genomeStyle)
cytoband <-
for (chr in unique(results$Chr)){
chrStr <- chr

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