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, 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,
		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 marker lists. The "successes" are the genes in the set, the "failures" are all other genes, and the drawing process typically involves picking the top N 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 for the number of genes.

Parameters

drawn_inside	Number of genes inside the set that were drawn.
num_inside	Total number of genes in the set.
num_outside	Total number of genes outside the set.
num_drawn	Number of genes that were drawn.
options	Further options for the calculation.

Returns

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