How to pass MAF file to dNdScv to detect cancer driven genes?

Question

[Kirill Kochnev]

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?

[zx8754]

Could you provide your example "MAF-file"?

Answer 1

[Inigo Martincorena]

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