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

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?

r dndscv maf mutations
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updated by Inigo Martincorena Inigo Martincorena • written by Kirill Kochnev • Kirill Kochnev

Could you provide your example "MAF-file"?

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written by zx8754 zx8754

1 answer

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

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written by Inigo Martincorena Inigo Martincorena

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