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