gseDomain {domainsignatures}R Documentation

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.

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.

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.
dist A named list containing similarity measures for all the resamples

Author(s)

Florian Hahne

See Also

gseDomain

Examples

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

[Package domainsignatures version 1.2.0 Index]