doEnrichment {MineICA} | R Documentation

## 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

[Package MineICA version 1.30.0 Index]