Using FACETS output as GISTIC 2.0 input

[andyjslee]

I would like to use FACETS output as GISTIC 2.0 input. Based on my reading of the comments in the Issues section of this Github repository, it seems that I can generate each seg.cn value (ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm) by the following ways:

Method 1: just use cnlr.median value
Method 2:
raw.copy.number = 2*2^(cnlr.median - diplogR)
seg.cn = log2(raw.copy.number) - 1

Which is the correct way of doing it?

Lastly, what is the best way to generate the markers file?

Thank you for your time and help!

[alexpenson]

I wouldn't use Method 2, if you want to adjust for the diploid log ratio, use cnlr.median - diplogR.
A third method is to use the log tcn values, which corresponds to also adjusting for the purity.

The markers are the input SNPs.

[veseshan]

Yes "cnlr.median - dipLogR" is the log(total copy number) unadjusted for purity which is what you want.

[andyjslee]

Thank you!

[HenrikBengtsson]

Yes "cnlr.median - dipLogR" is the log(total copy number) unadjusted for purity which is what you want.

@veseshan , I'm late to the game, but AFAIU, GISTIC 2.0 is not invariant to purity and doesn't make any attempts to estimate or adjust for it. Because of this, wouldn't you want to use a log(TCN) that is adjusted for purity as input to GISTIC 2.0?