MutSigCV output and coMut plots

Question

[A. Domingues]

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:

• my_results.categs.txt
• my_results.coverage.txt
• my_results.mutations.txt
• my_results.mutcateg_discovery.txt
• my_results.sig_genes.txt

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 MuTect, 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.

[fongchunchan]

Did you ever find an answer to Q1? I have the same question.

[A. Domingues]

Not really. At the time I sort of deduced what could be in each file, but I was never confident enough about it. In the meantime I've moved and never looked at it again. Good luck.

Answer 1

[A. Domingues]

There is now an R package that reproduces this type of plot, and much more:

GenVisR

May thanks to the Griffith Lab. Other options listed here.

[SG]

Is there a step by step guide to work with GenVisR for a non-bioinformatician?

[zlskidmore]

For the waterfall plot there is a nice tutorial here: How to create a mutation landscape (waterfall) plot with GenVisR

Answer 2

[jana]

RE Q1: There is a README.txt included in the installation package that describes the output files. You will find it here

Very useful discussion (though somewhat chaotic)

To summarize it:

• install instructions on the Broad Institute's web are no longer valid
• here is the latest MutSig2CV 1.4 version installation .tar
  • README.txt is included and worth reading
  • it covers installation and output files
• there is an on-line MutSigCV 1.3 version
  • here are links to exome_full192.coverage.txt, gene.covariates.txt, and mutation_type_dictionary_file.txt files that currently work
  • links on the GenePattern are not up to date

My main problem now is that on-line MutSigCV and desktop MutSigCV give very different results :)