how do I convert a vcf file for a GWAS study (using R package vcfR) I have a vcf file with individual level genetic data, that I read using the R package vcfR 

gen &lt;- read.vcfR('test.vcf')

Scanning file to determine attributes.
File attributes:
  meta lines: 9
  header_line: 10
  variant count: 152
  column count: 3798
Meta line 9 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
  Character matrix gt rows: 152
  Character matrix gt cols: 3798
  skip: 0
  nrows: 153
  row_num: 0
Processed variant: 153
All variants processed


How do I convert this file to a data frame that I can use for a GWAS or Mendelian Randomization study?

I was told that this should be a data frame where each column is a genetic variant and it take values 0, 1, or 2, depending on the number of "mutations".

I never worked with genetic data before and do not know much about genetics.
If you want to do GWAS or mendelian randomisation, you can do it with Plink (v2) which should be faster than R.