get_min_alpha | R Documentation |
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.
get_min_alpha(x)
x |
A 'dnapath_list' or 'dnapath' object from |
The minimum alpha level that can be used based on the number of permutations performed in the analysis.
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
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