PureCN Solution Heatmap values
1
0
Entering edit mode
twtoal ▴ 10
@twtoal-15473
Last seen 4 months ago
United States

I have a case where the heatmap of PureCN optimal purity/ploidy solutions for a sample shows the maximum likelihood solution (marked with a 1 on the heatmap) is located at what appears to NOT be a heatmap peak.  I examined the heatmap numbers (used PureCN:::.matrixTotalPloidyToTumorPloidy() to get the heatmap matrix), and I find that the matrix number located at the #1 solution peak doesn't match either the log.likelihood value or the total.log.likelihood value of the #1 solution.  Does the matrix factor in other numbers?

 

PureCN heatmap likelihoods • 1.2k views
ADD COMMENT
0
Entering edit mode
@markusriester-9875
Last seen 2.4 years ago
United States

Yes, the matrix is an approximation that does not try to assign integer copy numbers to segments yet. The idea is to start the Markov chain at various places that are likely close to local optima - the fitness landscape of this problem is so spiky it's hard to get a good mixing chain otherwise.

The number 1 should still be fairly close to a peak. If not, it might be a noisy, low purity or highly heterogeneous sample. Hard to diagnose from the distance.

ADD COMMENT

Login before adding your answer.

Traffic: 664 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6