Auto-detects PLINK2 (.pgen/.pvar[.zst]/.psam) or PLINK1 (.bed/.bim/.fam) format
and loads genotype data accordingly. Returns a numeric dosage matrix.
Usage
load_genotype_region(
genotype,
region = NULL,
keep_indel = TRUE,
keep_variants_path = NULL
)
Arguments
- genotype
Path to the genotype data file (without extension).
- region
The target region in the format "chr:start-end".
- keep_indel
Whether to keep indel SNPs.
- keep_variants_path
Path to a file listing variants to keep.
Value
A numeric dosage matrix (rows=samples, cols=variants).