Extract genome-wide significant independent loci

Filters a meta-analysis data frame to genome-wide significant variants, identifies independent loci via gwasRtools::get_loci(), and annotates each lead variant with the nearest gene via gwasRtools::get_nearest_gene(). Returns an empty tibble::tibble() when no variants pass the p-value threshold.

Usage

extract_loci(
  df,
  snp_col = RSID,
  chr_col = CHR,
  pos_col = POS_38,
  maf_col = EAF,
  beta_col = B,
  se_col = SE,
  p_col = p_value,
  p_threshold = 5e-08,
  build = 38,
  ...
)

Arguments

df

A data frame of meta-analysis results (e.g. output of meta_analyze_ivw()).

snp_col

Bare column name for rsid. Default RSID.

chr_col

Bare column name for chromosome. Default CHR.

pos_col

Bare column name for position. Default POS_38.

maf_col

Bare column name for minor allele frequency. Default EAF.

beta_col

Bare column name for effect size. Default B.

se_col

Bare column name for SE. Default SE.

p_col

Bare column name for p-value. Default p_value.

p_threshold

Genome-wide significance threshold. Default 5e-8.

build

Genome build for gene annotation (37 or 38). Default 38.

...

Additional arguments forwarded to gwasRtools::get_loci().

Value

A tibble::tibble() of independent lead variants with gene annotations, or an empty tibble if no variants pass the threshold.

Details

Extract genome-wide significant loci

Examples

if (FALSE) { # \dontrun{
loci <- extract_loci(meta_results, p_threshold = 5e-8)
} # }