phyper Namespace Reference

Compute hypergeometric tail probabilities. More...

Classes
struct	Options
	Options for compute(). More...

Functions
template<typename Count_ >
double	compute (Count_ drawn_inside, Count_ num_inside, Count_ num_outside, const Count_ num_drawn, const Options &options)

Detailed Description

Compute hypergeometric tail probabilities.

Function Documentation

compute()

template<typename Count_ >

double phyper::compute	(	Count_	drawn_inside,
		Count_	num_inside,
		Count_	num_outside,
		const Count_	num_drawn,
		const Options &	options )

Compute the tail probabilities for the hypergeometric distribution. It is intended for use in quantifying gene set enrichment in a list of top marker genes. The "successes" are the genes in the set, the "failures" are all other genes, and the drawing process typically involves selecting the top markers; our aim is to compute the p-value for enrichment of genes in the set among the top markers.

Template Parameters

Count_

Integer type of the number of genes.

Parameters

drawn_inside	Number of genes in the gene set that were selected as markers.
num_inside	Total number of genes in the gene set.
num_outside	Total number of genes outside the gene set.
num_drawn	Number of genes that were selected as top markers.
options	Further options for the calculation.

Returns

Probability of randomly selecting at least drawn_inside genes from the gene set, if Options::upper_tail = true. Otherwise, the probability of randomly selecting no more than drawn_inside genes from the gene set. These probabilities are log-transformed when Options::log = true.