test_cones_modules {martini} | R Documentation

## Calculate an empirical p-value for `find_cones` results.

### Description

Do a permutation-based test to assess the statistical significance of each of the modules obtained through shake. For a module of size k, k interconnected SNPs are picked `nperm` times, and their joint association score is calculated to come up with an estimation of the distribution.

### Usage

    test_cones_modules(cones, net, nperm = 1e+05)

### Arguments

`cones` | Results from `find_cones`.
`net` | The same SNP network provided to `find_cones`.
`nperm` | Integer with the name of permutations.

### Value

An empirical p-value for each of the SNP modules. Please, note that the minimum possible p-value from an empirical distribution is set to `1/(nperm+1)`. Modules composed by a single SNP will not have an empirical p-value.

### Examples

    gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi)
    cones <- search_cones(minigwas, gi)
    martini:::test_cones_modules(cones, gi, 100)

[Package martini version 1.2.0 Index]