vcf_theta — vcf_theta • VCFArrow

Calculates basic Watterson's theta and pi for all samples and for sample groups from VCFArrow format data.

Usage

vcf_theta(vcf_arrow, keep_groups = NULL)

Arguments

vcf_arrow: -> VCFArrow object
keep_groups: -> groups to retain, default NULL (character)

Value

list of statistics

Details

This function calculates Watterson's theta and pi for the entire VCFArrow object, and for groups of individuals whose grouping is indicated by the groups slot in the VCFArrow object. The statistics are accumulated chunk by chunk as running sums per group, so memory use does not grow with the number of variants, and chunks are processed in parallel when workers are set with vcf_set_workers().

Author

Tomas Hrbek April 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
vcf_theta(vcf)
#> $pi
#> [1] 0.3065724
#> 
#> $theta_w
#> [1] 0.3225428
#> 
#> $theta_g
#>    sample group n_ind   theta_w        pi
#> 1   Pv120    WA     5 0.2113146 0.1897392
#> 2   Pv126    GS     5 0.1916500 0.1751468
#> 3    Pv13    BS     5 0.1842761 0.1692308
#> 4    Pv14    GS     5 0.1916500 0.1751468
#> 5    Pv27    GS     5 0.1916500 0.1751468
#> 6    Pv28    GS     5 0.1916500 0.1751468
#> 7     Pv2    WA     5 0.2113146 0.1897392
#> 8    Pv31    WA     5 0.2113146 0.1897392
#> 9    Pv56    WA     5 0.2113146 0.1897392
#> 10   Pv62    BS     5 0.1842761 0.1692308
#> 11   Pv68    BS     5 0.1842761 0.1692308
#> 12   Pv73    BS     5 0.1842761 0.1692308
#> 13   Pv78    GS     5 0.1916500 0.1751468
#> 14   Pv79    BS     5 0.1842761 0.1692308
#> 15   Pv93    WA     5 0.2113146 0.1897392
#> 16  Pb2Jp    OG     3 0.1712101 0.1498553
#> 17 Pb2Scx    OG     3 0.1712101 0.1498553
#> 18  Pb1Rd    OG     3 0.1712101 0.1498553
#>