Genotype File Handle — GenotypeHandle-class • pecotmr

S4 container holding a path + format + metadata for lazy genotype access. Supports PLINK1 (.bed/.bim/.fam), PLINK2 (.pgen/.pvar/.psam), VCF/BCF, and GDS.

Slots

path: Character, file path. For a one-file-per-chromosome handle this is the chrom-meta file path (a display/provenance value); the per-chromosome payload files live in chromPaths.
format: Character, one of "plink1", "plink2", "vcf", "gds".
snpInfo: data.frame, SNP metadata read from the index/sidecar. For a sharded handle this is the union across chromosomes (row-bound in the order the shards were supplied), so snpIdx stays a single global index space.
nSamples: Integer, number of samples.
sampleIds: Character vector of sample identifiers.
pgenPtr: Opaque pointer for PLINK2 reader state (NULL otherwise).
chromPaths: Named character vector mapping canonical chromosome (e.g. "21", "X") to the per-chromosome payload path/prefix. Empty (character(0)) for a single-file handle; non-empty marks a one-file-per-chromosome (sharded) handle whose extraction is routed by chromosome.