MatrixEpistasis input format

Question

[Omics data mining]

Dear all,

I have identified some SNPs from two groups of cancer. I want to analyse the SNP-SNP interaction. I have SNPs in vcf format. I have converted vcf to plink (.map and .ped) format. But while working on "A quick toy example",I found input is snp matrix with numeric data type. How to define the input from vcf to MatrixEpistasis (I am new in area of epistasis).

I will appreciate all the suggestions

Thank you in advance

Archana