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
Hi there,
I read this in part Calling methods of the document:
However, My calculations using the formula
log2( (1 - purity) + purity * (0:4) / ploidy )are as follows: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