Hi FACETS developers,
When I use FACETS on my WES data, I realized that the ploidy estimate (fit$ploidy) can be much different from the CN segment profile. Below I attached an example:
As you can see, most large segments lie on CN2 or CN3 horizontal lines, but the ploidy given by FACETS is 5.14 (purity = 0.38). I just want to make sure this is not a bug. Maybe ploidy is inferred independent of absolute copy number, am I right?
If that is true, which one should I use as the "mean ploidy"?
The value from fit$ploidy
The mean value of absolute CNs of all segments, weighted by the segment length
Do you have any recommendation? Thanks in advance!
Hi FACETS developers, When I use FACETS on my WES data, I realized that the ploidy estimate (fit$ploidy) can be much different from the CN segment profile. Below I attached an example:
As you can see, most large segments lie on CN2 or CN3 horizontal lines, but the ploidy given by FACETS is 5.14 (purity = 0.38). I just want to make sure this is not a bug. Maybe ploidy is inferred independent of absolute copy number, am I right?
If that is true, which one should I use as the "mean ploidy"?
Do you have any recommendation? Thanks in advance!
Best Yang