set_vcf_groups — set_vcf_groups • VCFArrow

Associate samples with group info based on "strt" file

Usage

set_vcf_groups(vcf_arrow, data_path, strt = "strata")

Arguments

vcf_arrow: -> VCFArrow object
data_path: -> path to data (where strata are located)
strt: -> file with 2+ columns, one id column and one pop column (tsv file, header = TRUE)

Value

vcf_arrow object with groups slot filled

Details

This function creates list of factors of sample-to-group assignments and groups based on a strata and group file. The strt is a tsv file with 2+ columns, with 2 columns named 'id' and 'pop'. By default strt is named 'strata' and found in the datapath where the VCF file is found.

Author

Tomas Hrbek April 2026

Examples

f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
                 package = "VCFArrow")
vcf <- set_vcf_groups(read_vcf(f), data_path = dirname(f),
                      strt = "strata")
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
table(vcf@groups)
#> 
#> BS GS OG WA 
#>  5  5  3  5