test_cones_modules: Calculate an empirical p-value for 'find_cones' results.
In martini: GWAS Incorporating Networks

Description Usage Arguments Value Examples

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.

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

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

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.

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