hyperg_test {pathfindR}

Hypergeometric Distribution-based Hypothesis Testing

Description

Hypergeometric Distribution-based Hypothesis Testing

Usage

hyperg_test(term_genes, chosen_genes, background_genes)

Arguments

term_genes

vector of genes in the selected term gene set

chosen_genes

vector containing the set of input genes

background_genes

vector of background genes (i.e. universal set of genes in the experiment)

Details

To determine whether the chosen_genes are enriched (compared to a background pool of genes) in the term_genes, the hypergeometric distribution is assumed and the appropriate p value (the value under the right tail) is calculated and returned.

Value

the p-value as determined using the hypergeometric distribution.

Examples

hyperg_test(letters[1:5], letters[2:5], letters)
hyperg_test(letters[1:5], letters[2:10], letters)
hyperg_test(letters[1:5], letters[2:13], letters)