Filter variants by LD Reference

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.

Examples

meta <- system.file("extdata", "ld_reference", "ld_meta_file.tsv",
  package = "pecotmr")
filterVariantsByLdReference(
  variantIds = c("chr22:16050000:A:G", "chr22:17000000:C:T"),
  ldReferenceMetaFile = meta)
#> 2 out of 2 total variants dropped due to absence on the reference LD panel.
#> $data
#> character(0)
#> 
#> $idx
#> integer(0)
#>