doEnrichment: Runs enrichment analysis of contributing genes

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

Runs enrichment analysis of contributing genes

Description

doEnrichment This internal function is called by hypergeoAn and runs hypergeometric tests through function hyperGTest to associate the contributing genes of a component to gene sets.

Usage

  doEnrichment(compSel, chip, onto, hgCutoff, cond,
    universe, path, db, pack.annot.EID, Slist, it, cutoff,
    entrez2symbol)

Arguments

compSel	A list containing three elements compSel the projection values of contributing genes that were selected based on their absolute projection compSel_neg the projection values of contributing genes that have negative projections compSel_pos the projection values of contributing genes that have positive projections
chip	The annotation package
onto	A string specifying the GO ontology to use. Must be one of 'BP', 'CC', or 'MF', see GOHyperGParams. Only used when argument db is 'GO'.
hgCutoff	The p-value threshold
cond	A logical indicating whether the calculation should conditioned on the GO structure, see GOHyperGParams.
universe	The universe for the hypergeometric tests, see GOHyperGParams.
path	The path where results will be saved
db	The used database to use ('GO' or 'KEGG')
pack.annot.EID	The name of the environment of the annotation package containing the annotation for Entrez Gene.
Slist	The list of gene projections across all components
it	The index of the component
cutoff	The threshold applied on the gene projections, used to select the contributing genes
entrez2symbol	A vector of all gene Symbols involved in the analysis indexed by their Entrez Gene IDs. It is only used when annotation(params) is empty, and allows to associate gene sets to Symbols.

Value

Object of class GOHyperGResult-class

Author(s)

Anne Biton

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.