get_min_alpha: Get the minimum alpha level for the permutation test

Description Usage Arguments Value Examples

View source: R/summary.R

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

1

Arguments

x

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

Value

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

Examples

1
2
3
4
5
6
7
8
data(meso)
data(p53_pathways)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   groups = meso$groups, n_perm = 5)
get_min_alpha(results) # 1 / (5 + 1) = 0.167
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   groups = meso$groups, n_perm = 10)
get_min_alpha(results) # 1 / (10 + 1) = 0.091

dnapath documentation built on Dec. 11, 2021, 9:54 a.m.