orderedHypergeometric {ActivePathways}

Ordered Hypergeometric Test

Description

Perform a series of hypergeometric tests (a.k.a. Fisher's Exact tests), on a ranked list of genes ordered by significance against a list of annotation genes. The hypergeometric tests are executed with increasingly larger numbers of genes representing the top genes in order of decreasing scores. The lowest p-value of the series is returned as the optimal enriched intersection of the ranked list of genes and the biological term (pathway).

Usage

orderedHypergeometric(genelist, background, annotations)

Arguments

genelist

Character vector of gene names, assumed to be ordered by decreasing importance. For example, the genes could be ranked by decreasing significance of differential expression.

background

Character vector of gene names. List of all genes used as a statistical background (i.e., the universe).

annotations

Character vector of gene names. A gene set representing a functional term, process or biological pathway.

Value

a list with the items:

p_val

The lowest obtained p-value

ind

The index of genelist such that genelist[1:ind] gives the lowest p-value

Examples

   orderedHypergeometric(c('HERC2', 'SP100'), c('PHC2', 'BLM', 'XPC', 'SMC3', 'HERC2', 'SP100'),
                         c('HERC2', 'PHC2', 'BLM'))