Question: MutSigCV output and coMut plots
3
gravatar for A. Domingues
5.3 years ago by
A. Domingues2.2k
Dresden, Germany
A. Domingues2.2k wrote:

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 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.

mutsigcv snp comut plot variants • 6.5k views
ADD COMMENTlink modified 10 months ago by jana70 • written 5.3 years ago by A. Domingues2.2k

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

ADD REPLYlink written 4.5 years ago by fongchunchan10

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. 

ADD REPLYlink written 4.5 years ago by A. Domingues2.2k
6
gravatar for A. Domingues
3.6 years ago by
A. Domingues2.2k
Dresden, Germany
A. Domingues2.2k wrote:

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.

ADD COMMENTlink written 3.6 years ago by A. Domingues2.2k
1
gravatar for jana
10 months ago by
jana70
jana70 wrote:

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:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by jana70
0
gravatar for SG
3.3 years ago by
SG0
SG0 wrote:

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

ADD COMMENTlink written 3.3 years ago by SG0

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

ADD REPLYlink written 3.1 years ago by zlskidmore290
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