VCFArrow S4 class — VCFArrow-class • VCFArrow

S4 class holding VCF data. Variant metadata are kept in memory while genotypes are stored on disk as an Apache Arrow dataset and loaded lazily. Objects are created with read_vcf().

Slots

header: Complete VCF header (character).
info: INFO field of each variant (character).
format: FORMAT field of each variant (data.frame).
variants: CHROM, POS, ID, REF, ALT, QUAL, FILTER and precalculated per-variant metrics (data.frame).
gt: Arrow dataset of genotypes in long format.
samples: Sample names (character).
groups: Group assignment of each sample (character).
path: Location of the on-disk Arrow dataset (character).
finalizer_env: Environment used to clean up path on garbage collection.
loci: CHROM, POS, REF and ALT of every variant of the source VCF, row i describing .row_id i; never filtered, so variants can be identified (e.g. by vcf_bind()) even after they were removed from variants (data.frame).
invariant_removed: Variants removed as invariant, with their metadata (data.frame).

Author

Tomas Hrbek April 2026