Filters a vector of variant IDs to those present in the LD reference panel.
Auto-detects the reference type (PLINK2, PLINK1, or pre-computed LD metadata).
Usage
filterVariantsByLdReference(variantIds, ldReferenceMetaFile, keepIndel = TRUE)
Arguments
- variantIds
variant names in the format chr:pos:ref:alt.
- ldReferenceMetaFile
Path to LD metadata file or PLINK prefix.
- keepIndel
Whether to keep indel variants. Default TRUE.
Value
A list with:
- data
Character vector of filtered variant IDs.
- idx
Integer vector of indices into the original variantIds.