dnapath (version 0.7.6)

get_min_alpha: Get the minimum alpha level for the permutation test

Description

This method is used internally by several methods to determine the minimum significance threshold (alpha value) that can be applied to the permutation p-values obtained in the differential network analysis.

Usage

get_min_alpha(x)

Value

The minimum alpha level that can be used based on the number of permutations performed in the analysis.

Arguments

x

A 'dnapath_list' or 'dnapath' object from dnapath.

Examples

data(meso)
data(p53_pathways)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   group_labels = meso$groups, n_perm = 5)
get_min_alpha(results) # 1 / (5 + 1) = 0.167
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   group_labels = meso$groups, n_perm = 10)
get_min_alpha(results) # 1 / (10 + 1) = 0.091