how do I convert a vcf file for a GWAS study (using R package vcfR)

Question

I have a vcf file with individual level genetic data, that I read using the R package vcfR

gen <- 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.

Answer 1

If you want to do GWAS or mendelian randomisation, you can do it with Plink (v2) which should be faster than R.