I am using the lastest MutSigCV v1.4, and trying to implement the "CoMut plot" to visualize the results. However, the MutSigCv documenttation only describes the content of one the results files (my_results.sig_genes.txt), but there are 5 files that MutSigCV outputs:
Yes, I did ask the developers but... *tumble-weed*
Q1: Where can I find an explanation for the data in the other 4 files?
As I mentioned, I am replicating some parts of coMut, which has generated a couple of questions in Biostar (here and here). The plots representing the top mutated genes (left of coMut) and type of mutation per sample (bottom) were easy using data from MutSigCV - using data in the files my_experiment.sig_genes.txt and my_experiment.mutations.txt
However without having a precise explanation of the MutSigCV output, I cannot proceed further.
Q2: Which data is used for the remaining components of the plot? I have a suspicion that the top bar plot (number of mutations/Mb) uses data from MuTec, but no idea about the other 2 components. My guess is that some of that is buried in the MutSigCV output files but can't figure out where.