etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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A question about purity assumption in the Docs #840

Open RysBen opened 10 months ago

RysBen commented 10 months ago

Hi there,

I read this in part Calling methods of the document:

But the outer cutoffs of -1.1 and +0.7 assume 100% purity, ...

However, My calculations using the formula log2( (1 - purity) + purity * (0:4) / ploidy ) are as follows:

copy numbers purity=0.2 purity=0.5 purity=1
0 (del) -0.32-0.1 -1.0-0.1 -Inf
1 (loss) -0.15-0.1 -0.4-0.1 -1.0-0.1
2 (neutral) 0.0 0.0 0
3 (gain) 0.13+0.1 0.3+0.1 0.6+0.1
4 (amp) 0.26+0.1 0.6+0.1 1.0+0.1

Note: 0.1 is allowed for random noise according the code.

It looks like the purity assumption of outer cutoffs should be 50%, not 100%.

Could you point out where my understanding is wrong?

Thanks