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gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
GNU General Public License v3.0
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Non-human chromosome length #77

Open peterpdu opened 4 years ago

peterpdu commented 4 years ago

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.

Screen Shot 2019-09-04 at 10 35 38 AM

Thanks, Peter

gavinha commented 4 years ago

Hi @peterpdu

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

https://github.com/gavinha/TitanCNA/blob/c4f94ee10e74e83869c9585501a3dacfee3464cc/scripts/R_scripts/titanCNA.R#L184-L189

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

-Gavin