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NKI-CCB / DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
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how to create the input file? #18

Closed stroke1989 closed 1 year ago

stroke1989 commented 1 year ago

Hi, Thanks for this awesome tool, I tried to use DISCOVER to analyze my data, but I'm not a bioinformatist, I don't know how to create the input file， a matrix as below:

Snipaste_2022-07-28_21-17-12

Hope your response! Appreciate!

scanisius commented 1 year ago

The mutation matrix that you need for DISCOVER has genes in the rows and tumours in the columns. The values in that matrix are either 0 or 1, where 1 indicates a mutation in the particular gene and tumour, and 0 indicates the absence of such a mutation.

The steps you need to take to create the input matrix for DISCOVER will depend on the type of data you start with, so I can't comment on your particular situation. Have a look at the description in #7 for an example of how to create a mutation matrix from TCGA mutation data. This description expects the mutation data to be available in MAF format. If your data are stored in VCF format instead, you might use a tool like vcf2maf to create a MAF file.

scanisius commented 1 year ago

This issue has been inactive for a while now, so I am closing it. Please open a new issue if you are still experiencing problems with DISCOVER.