test_cones_modules {martini} | R Documentation |
find_cones
results.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.
test_cones_modules(cones, net, nperm = 1e+05)
cones |
Results from |
net |
The same SNP network provided to |
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.
gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi) cones <- search_cones(minigwas, gi) martini:::test_cones_modules(cones, gi, 100)