doEnrichment: Runs enrichment analysis of contributing genes

Description Usage Arguments Value Author(s)

View source: R/functions_enrich.R

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

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  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


Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.