cnvkit
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A question about purity assumption in the Docs
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