vcf2eigenstrat

Converts a VCFArrow object to Eigenstrat format infile

Usage

vcf2eigenstrat(vcf_arrow, out_file, keep_groups = NULL, sex = NULL)

Arguments

vcf_arrow

-> VCFArrow object

out_file

-> output file prefix; extensions are added automatically, no default (character)

keep_groups

-> groups to retain, default NULL (character)

sex

-> sex of the individual, default = U (undefined) (character)

Value

Invisibly returns the input VCFArrow object; called for its side effect of writing out_file.

Details

This function converts a VCFArrow object to an external BayesAss formatted file. Writing occurs in chunks whose size is determined by the read_vcf() function. Larger chunks result in faster writing speeds. If no groups are defined, the default behavior is to use all groups.

Author

Tomas Hrbek May 2026

Examples

f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
                 package = "VCFArrow")
vcf <- read_vcf(f) |> set_vcf_groups(dirname(f))
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
vcf2eigenstrat(vcf, out_file = file.path(tempdir(), "eigenstrat_in"))
#> ℹ Building EIGENSTRAT: 9313 variants x 18 samples (0 MiB raw storage)
#> ℹ Writing EIGENSTRAT files...
#> ✔ EIGENSTRAT fileset written to /tmp/RtmpSpcr9J/eigenstrat_in.geno, /tmp/RtmpSpcr9J/eigenstrat_in.ind, /tmp/RtmpSpcr9J/eigenstrat_in.snp