Get significant loci — get_loci • ggwas

Extract variants below a p-value threshold, with optional clumping to return only independent lead SNPs.

Usage

get_loci(data, p_threshold = 5e-08, clump = TRUE, clump_window = 1e+06)

Arguments

data: A gwas_data object or data.frame.
p_threshold: P-value threshold (default 5e-8).
clump: If TRUE, apply window-based clumping.
clump_window: Clumping window in bp (default 1 Mb).

Value

A data.frame of significant variants.

Examples

data(example_gwas)
get_loci(example_gwas, p_threshold = 0.001)
#> A gwas_data object: 448 variants across 22 chromosomes
#>   Min p-value: 1.19e-14
#>   Lambda GC:   31.988
#>   Columns:     CHR, BP, SNP, P, BETA, SE, A1, A2, AF