assess_vcf_missing_data — assess_vcf_missing

Quantifying missing data of all samples in VCF

Usage

assess_vcf_missing_data(vcf_arrow, res_path, species, project, details = TRUE)

Arguments

vcf_arrow: -> VCFArrow object
res_path: -> path to results (directory for output dataframe and plots)
species: -> sample name for plot (character)
project: -> project name / base output file name (character)
details: -> flag for adding project name into figure title, default TRUE (Boolean)

Value

dataframe and plot of missing data for each sample in VCF

Details

This function generates a dataframe of absolute and relative missing data per sample, and a plot of relative missing data % per sample.

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
assess_vcf_missing_data(vcf, res_path = tempdir(),
                        species = "Phyllomedusa vaillantii",
                        project = "vaillantii")