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griffithlab / GenVisR

Genome data visualizations
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cnFreq does not reflect total number of samples #352

Open gaiusjaugustus opened 5 years ago

gaiusjaugustus commented 5 years ago

I am using cnFreq to plot copy number change in 39 cancer samples. However, several samples don't have any copy number changes. This means there aren't segments in the data for them, but I still want cnFreq to take those samples into account.

For example, if only 15 (of 39) samples have any alterations, and 10 have alterations on chromosome 1, cnFreq shows alterations in 66% (10/15) of patients instead of 26% (10/39).

Is there a way to specify the number of samples, or another workaround?

Thanks.

gaiusjaugustus commented 5 years ago

I was able to work around this by adding fake segments (without of range segmeans and/or on chr X, which is not within my data) for all samples that were not represented.

If there's a simpler way, I'd love to know. But this workaround fixed my current issue.

zlskidmore commented 5 years ago

thanks for the issue @gaiusjaugustus, sorry was on vacation, I think a few of the other functions have the ability to specify samples explicitly, i'll look into adding something like that here (explicitly setting the denominator). I'm going to leave this open as an enhancement.