git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 05/02/2013 22:15:53
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+\name{doEnrichment}
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+\alias{doEnrichment}
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+\title{Runs enrichment analysis of contributing genes}
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+\usage{
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+ doEnrichment(compSel, chip, onto, hgCutoff, cond, |
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+ universe, path, db, pack.annot.EID, Slist, it, cutoff, |
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+ entrez2symbol) |
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+} |
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+\arguments{
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+ \item{compSel}{A list containing three elements
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+ \describe{ \item{compSel}{the projection values of
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+ contributing genes that were selected based on their |
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+ absolute projection} \item{compSel_neg}{the projection
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+ values of contributing genes that have negative |
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+ projections} \item{compSel_pos}{the projection values of
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+ contributing genes that have positive projections}}} |
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+ |
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+ \item{chip}{The annotation package}
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+ |
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+ \item{onto}{A string specifying the GO ontology to use.
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+ Must be one of 'BP', 'CC', or 'MF', see |
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+ \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.
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+ Only used when argument \code{db} is 'GO'.}
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+ |
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+ \item{hgCutoff}{The p-value threshold}
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+ |
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+ \item{cond}{A logical indicating whether the calculation
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+ should conditioned on the GO structure, see |
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+ \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}
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+ |
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+ \item{universe}{The universe for the hypergeometric
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+ tests, see |
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+ \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}
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+ |
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+ \item{path}{The path where results will be saved}
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+ |
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+ \item{db}{The used database to use ('GO' or 'KEGG')}
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+ |
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+ \item{pack.annot.EID}{The name of the environment of the
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+ annotation package containing the annotation for Entrez |
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+ Gene.} |
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+ |
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+ \item{Slist}{The list of gene projections across all
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+ components} |
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+ |
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+ \item{it}{The index of the component}
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+ |
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+ \item{cutoff}{The threshold applied on the gene
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+ projections, used to select the contributing genes} |
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+ |
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+ \item{entrez2symbol}{A vector of all gene Symbols
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+ involved in the analysis indexed by their Entrez Gene |
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+ IDs. It is only used when \code{annotation(params)} is
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+ empty, and allows to associate gene sets to Symbols.} |
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+} |
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+\value{
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+ Object of class \code{GOHyperGResult-class}
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+} |
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+\description{
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+ doEnrichment This internal function is called by |
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+ \code{hypergeoAn} and runs hypergeometric tests through
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+ function \code{hyperGTest} to associate the contributing
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+ genes of a component to gene sets. |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+\keyword{internal}
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+ |