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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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Best likelihood or "average" tree? #61

Open detorrentel opened 7 years ago

detorrentel commented 7 years ago

Hi,

I used phyloWGS to generate a tree from a breast cancer patient and now I would like to know how to choose the final result. I saw that in another issue you said to order by the likelihood (LLH) is it the column nlgLH? So I should take the tree with the highest LLH? What if several of them have the same value? In another issue I see that you talked about getting the "average" tree using: https://github.com/morrislab/smchet-challenge/tree/master/create-smchet-report

What is the best way to go?

Thank you!

detorrentel commented 7 years ago

I also see that in tree summaries the title of the second figure (clustering vs branching) have "best tree: 446" so is it the one corresponding to the best likelihood?

quaidmorris commented 7 years ago

The best tree is the one most similar to all the other trees. We are in the midst of developing a new way to represent the solutions from PWGS but it will be a few months before that is available.

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On Jun 14, 2017, at 4:01 PM, detorrentel notifications@github.com wrote:

I also see that in tree summaries the title of the second figure (clustering vs branching) have "best tree: 446" so is it the one corresponding to the best likelihood?

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detorrentel commented 7 years ago

So for now what do you recommend to take as the solution tree?

quaidmorris commented 7 years ago

Take the best tree for now.

Q

Quaid Morris, PhD Associate Professor, The Donnelly Centre Departments of Molecular Genetics and Computer Science 160 College St, Rm 616 Toronto ON, M5S 3E1 Canada http://morrislab.ca http://morrislab.med.utoronto.ca cell: (416) 220 5796

On Thu, Jun 15, 2017 at 1:22 AM, detorrentel notifications@github.com wrote:

So for now what do you recommend to take as the solution tree?

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AmitDeshwar commented 7 years ago

@detorrentel A better summary of the sampled trees can be found by using the SMC-Het report generation code found here: https://github.com/morrislab/smchet-challenge/tree/master/create-smchet-report