8.6 Reading in genotype data

Because VCF format can be hard to work with, we’ll use the vcfR package to manipulate our genotype data.

# load the VCF with vcfR
vcf <- read.vcfR("genotypes_subset.vcf")

## Scanning file to determine attributes.
## File attributes:
##   meta lines: 27
##   header_line: 28
##   variant count: 72
##   column count: 185
## Meta line 27 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 185
##   skip: 0
##   nrows: 72
##   row_num: 0
## Processed variant: 72
## All variants processed