HLA-aware PLINK clumping (Yet implemented)

Simple wrapper: "none" -> drop HLA (chr6:25–34Mb), clump non-HLA only "all" -> keep all HLA (no clump), clump non-HLA, then union "just_clump" -> clump all variants together

Usage

plink_clump_hla_aware(
  bfile,
  hla_keep = c("all", "none", "just_clump"),
  output,
  plink_bin = plinkbinr::get_plink_exe()
)

Arguments

bfile

PLINK bfile for LD reference.

hla_keep

One of c("all","none","just_clump").

output

Output prefix; expects {output}.clump.txt.

plink_bin

Path to PLINK.

Value

Character vector of kept SNPs; also writes {output}.kept.snps.txt.

Details

Input: {output}.clump.txt with columns "SNP","P". Defaults follow common PRS C+T: –clump-p1 1, –clump-p2 1, –clump-r2 0.1, –clump-kb 250.