Non-human chromosome length

[peterpdu]

Hi Gavin,

I'm running TitanCNA/ichorCNA on mouse exome data with the latest version of TitanCNA/ichorCNA, and the plots for ichorCNA have the incorrect chromosome length. This was not a problem with an older version of ichorCNA, so I was wondering if I could provide chromosome length files somewhere.

Thanks,
Peter

[gavinha]

Hi @peterpdu

You might want to consider modifying the following lines to use the mm genome

TitanCNA/scripts/R_scripts/titanCNA.R

Lines 184 to 189 in c4f94ee

	bsg <- paste0("BSgenome.Hsapiens.UCSC.", genomeBuild)
	if (!require(bsg, character.only=TRUE, quietly=TRUE, warn.conflicts=FALSE)) {
	seqinfo <- Seqinfo(genome=genomeBuild)
	} else {
	seqinfo <- seqinfo(get(bsg))
	}

This is untested and may cause issues throughout the rest of the main R script.

-Gavin