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 |
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]