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junseonghwan / PhylExAnalysis

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How to interpret the results #7

Open thestarocean opened 1 year ago

thestarocean commented 1 year ago

After running Phylex, there seem to be multiple chain folders, each having several joint trees. How do we determine which of the trees as the final results? Or there is additional step to merge these results?

junseonghwan commented 1 year ago

There is a function FindBestRep in PhylExR package. You just have to specify the root directory containing each of the chains.

Example here: https://github.com/junseonghwan/PhylExAnalysis/blob/5bafad3fb6dc60e4144b18e85bbdba47a9a04fe7/Rscripts/HGSOC_SS3_PhyloPhenoAnalysis.R#L35

thestarocean commented 1 year ago

Thank you very much for your help. It seems that joint tree0 from selected chain is the final result since the code stated that:

datum2node <- read. Table(paste(chain_path, "/joint/tree0/datum2node.tsv"

Is that correct?

junseonghwan commented 1 year ago

That is correct. tree0/ contains the corresponds to the tree with the highest likelihood.