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 1.0.0 Index]