interactions {phenopath} | R Documentation |
Computes a tidy data frame of the interaction effects, pathway scores, and significance for each gene and covariate interaction.
interactions(phenopath_fit, n = 3)
phenopath_fit |
An object returned by a call to |
n |
The number of standard deviations away from 0 the posterior of the interaction effect sizes should be to be designated as significant |
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
sim <- simulate_phenopath() fit <- phenopath(sim$y, sim$x, elbo_tol = 1e-2) interactions(fit)