domainsignatures (version 1.32.0)

gseDomain: Geneset enrichment based on InterPro domain signatures

Description

Compute the similarity to pathways specified trough dataSource for a set of entrezgene identifiers.

Usage

gseDomain(dataSource, geneset, n=10000, verbose=TRUE, samples=FALSE)

Arguments

dataSource

Object of class ipDataSource containing pathway and InterPro domain mappings

geneset

Character vector of entrezgene identifiers

n

Number of subsampling iterations

verbose

Toggle progress report

samples

Logical indicating whether to return the similarity measures for all the resamples.

Value

A list with items

similarity

Named vector of similarity measures for each pathway

pvalue

The p-values of similarity to each pathway. A named vector.

and optional item (if samples=TRUE)

dist

A named list containing similarity measures for all the resamples

Details

Use this function to compute p-values for similarity of the domain signature of a gene set to all signatures of the pathways defined in dataSource. You should have created dataSource using either function dataSource or getKEGGdata.

See Also

gseDomain

Examples

## see Vignette of this package for examples how to use this function