GWAS Summary Statistics

Standardized container for GWAS summary statistics. SNP positions are stored as a GRanges object, with effect sizes, standard errors, and sample sizes as metadata columns.

Slots

sumstats

A GRanges object with required metadata columns:

SNP

Character, SNP identifier (rsID or chr:pos:ref:alt)

A1

Character, effect allele

A2

Character, non-effect allele

Z

Numeric, z-score (BETA/SE)

N

Numeric, sample size (per-SNP or constant)

Optional metadata columns: MAF, INFO, BETA, SE, P.

genome

Character string for genome build.

trait_name

Character string for trait identifier.

var_y

Numeric, phenotype variance. For case-control studies this is 1 / (phi * (1 - phi)) where phi = n_case / n. For quantitative traits, typically 1 or NULL.