Implementation on ICGC data

[mortunco]

Dear @collinmelton ,

Thank you for coming with this method. It is helping me greatly in my thesis and publication(hopefully).

I am looking for a mutation enrichment in TF proximity in ~200 patients in breast cancer. I think I can use the method suggested in the paper with making couple changes.
Such as;

1. I have sparse matrix so only few of my patients ( mostly 2) have a mutation in the similar region. So can I get over this step ?
2. Can I define "the regions" as the locations of my TF bindings location ? (~750 bp )
3. If all of the answers are okay. Could you guide me to create proper input for the code. I dont know how to create covarity inputs.

I am using ICGC consensus mutation calling data for breast cancer so I have my data in VCF format.

Thank you very much for your help,

Best regards,

Tunc.