Question: How to pass MAF file to dNdScv to detect cancer driven genes?
1
gravatar for Kirill Kochnev
19 months ago by
Moscow
Kirill Kochnev10 wrote:

Hello everyone.

I have a MAF-file with mutations from cbioportal. I want to detect cancer driver genes using R package dNdScv. Could you help me with using MAF file as dNdScv input? Should I convert MAF to another format?

mutations dndscv R maf • 738 views
ADD COMMENTlink modified 17 months ago by Inigo Martincorena190 • written 19 months ago by Kirill Kochnev10

Could you provide your example "MAF-file"?

ADD REPLYlink modified 19 months ago • written 19 months ago by zx87549.4k
2
gravatar for Inigo Martincorena
17 months ago by
Sanger Institute, Cambridge, UK
Inigo Martincorena190 wrote:

Hello, Yes, to run dNdScv you need to provide the mutations in a simple 5-column dataframe, with the following columns: sampleID, chromosome, position, reference base, mutant base. You can follow the example in the tutorial below:

http://htmlpreview.github.io/?http://github.com/im3sanger/dndscv/blob/master/vignettes/dNdScv.html

ADD COMMENTlink written 17 months ago by Inigo Martincorena190
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