interactions: Tidy summary of interactions

In phenopath: Genomic trajectories with heterogeneous genetic and environmental backgrounds

Description

Computes a tidy data frame of the interaction effects, pathway scores, and significance for each gene and covariate interaction.

Usage

interactions(phenopath_fit, n = 3)

Arguments

phenopath_fit	An object returned by a call to phenopath
n	The number of standard deviations away from 0 the posterior of the interaction effect sizes should be to be designated as significant

Value

A data frame with the following columns:

• feature The feature (usually gene)

• covariate The covariate, specified from the order originally supplied to the call to phenopath

• interaction_effect_size The effect size of the interaction (beta from the statistical model)

• significant Boolean for whether the interaction effect is significantly different from 0

• chi The precision of the ARD prior on beta

• pathway_loading The pathway loading lambda, showing the overall effect for each gene marginalised over the covariate

Examples

sim <- simulate_phenopath() 
fit <- phenopath(sim$y, sim$x, elbo_tol = 1e-2)
interactions(fit)

phenopath documentation built on Nov. 8, 2020, 6:53 p.m.