Question: How to pass MAF file to dNdScv to detect cancer driven genes?
1
gravatar for Kirill Kochnev
3 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 • 221 views
ADD COMMENTlink modified 5 weeks ago by Inigo Martincorena170 • written 3 months ago by Kirill Kochnev10

Could you provide your example "MAF-file"?

ADD REPLYlink modified 3 months ago • written 3 months ago by zx87546.8k
2
gravatar for Inigo Martincorena
5 weeks ago by
Sanger Institute, Cambridge, UK
Inigo Martincorena170 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 5 weeks ago by Inigo Martincorena170
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