Compare nested PheWAS specifications on identical samples

Each phenotype is fitted twice on the exact same complete-case rows. The adjusted specification may differ from the base specification only by its analysis ID and by adding covariates. BH and Bonferroni values are then recomputed over the mutually successful testing universe.

Usage

run_phewas_contrast(data, base_spec, adjusted_spec, phenotype_ids = NULL)

Arguments

data

Analysis-ready individual-level data.

base_spec, adjusted_spec

Nested phewas_spec objects.

phenotype_ids

Optional subset of phenotype values.

Value

A phewas_contrast whose associations element contains paired estimates, changes, and shared-universe corrections.