R: Get the minimum alpha level for the permutation test

get_min_alpha {dnapath} | R Documentation

## 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)

### 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

    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

[Package dnapath version 0.7.4 Index]