interactions {phenopath} | R Documentation

## Tidy summary of interactions

### 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)

[Package phenopath version 1.8.0 Index]