Match GWAS SNPs against a reference SNP list — snp_match

Matches variants in sumstats against info_snp by rsid, effect allele (a1), and other allele (a0). Optionally removes ambiguous SNPs (A/T and C/G), performs strand flipping, and reverses allele coding.

Usage

snp_match_munge(
  sumstats,
  info_snp,
  strand_flip = TRUE,
  join_by_pos = TRUE,
  remove_dups = TRUE,
  match.min.prop = 0.2,
  return_flip_and_rev = FALSE
)

Arguments

sumstats: A data frame of GWAS summary statistics. Must contain columns rsid, a0, a1, and beta.
info_snp: A data frame of reference SNPs. Must contain columns rsid, a0, and a1.
strand_flip: Logical; if TRUE (default), remove ambiguous SNPs (A/T, C/G) and attempt strand flipping.
join_by_pos: Logical; if TRUE, also join by position. Default TRUE.
remove_dups: Logical; if TRUE (default), remove duplicate rsid entries after matching.
match.min.prop: Minimum proportion of variants that must match. Default 0.2. An error is raised if fewer variants match.
return_flip_and_rev: Logical; if TRUE, retain the _FLIP_ and _REV_ indicator columns in the output. Default FALSE.

Value

A data frame of matched variants ordered by chromosome.

Details

Match and munge SNPs against a reference panel

Examples

if (FALSE) { # \dontrun{
matched <- snp_match_munge(
  sumstats = my_sumstats,
  info_snp = hm3_snps
)
} # }