Anne Biton authored on 23/04/2020 18:30:14
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\item{icaSet}{An object of class \code{IcaSet}}
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\item{params}{An object of class
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- \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
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+ \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
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containing the parameters of the analysis} |
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\item{path}{The path where results will be saved}
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Runs an enrichment analysis of the contributing genes |
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associated with each component, using the function |
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\code{hyperGTest} of package
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- \code{\link[GOstats]{GOstats}}. The easiest way to run
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+ \code{\link{GOstats}}. The easiest way to run
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enrichment analysis is to use function |
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\code{\link{runEnrich}}.
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} |
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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new file mode 100644 |
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+\name{hypergeoAn}
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+\alias{hypergeoAn}
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+\title{Runs an enrichment analysis per component using package \code{\link{GOstats}}.}
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+\usage{
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+ hypergeoAn(icaSet, params, |
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+ path = paste(resPath(params), "GOstatsEnrichAnalysis/", sep = "/"), |
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+ SlistSel, hgCutoff = 0.01, db = "go", onto = "BP", |
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+ cond = TRUE, universe, entrez2symbol) |
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+} |
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+\arguments{
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+ \item{icaSet}{An object of class \code{IcaSet}}
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+ |
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+ \item{params}{An object of class
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+ \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
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+ containing the parameters of the analysis} |
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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{SlistSel}{A list of contributing gene projection
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+ values per component. Each element of the list |
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+ corresponds to a component and is restricted to the |
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+ features or genes exceeding a given threshold. If |
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+ missing, is computed by the function.} |
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+ |
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+ \item{hgCutoff}{The p-value threshold}
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+ |
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+ \item{db}{The database to be used (\code{"GO"} or
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+ \code{"KEGG"})}
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+ |
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+ \item{onto}{A character specifying the GO ontology to
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+ use. Must be one of \code{"BP"}, \code{"CC"}, or
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+ \code{"MF"}, see
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+ \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.
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+ Only used when argument \code{db} is \code{"GO"}.}
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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{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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+\description{
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+ Runs an enrichment analysis of the contributing genes |
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+ associated with each component, using the function |
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+ \code{hyperGTest} of package
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+ \code{\link[GOstats]{GOstats}}. The easiest way to run
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+ enrichment analysis is to use function |
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+ \code{\link{runEnrich}}.
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+} |
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+\details{
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+ An annotation package must be available in |
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+ \code{annotation(icaSet)} to provide the contents of the
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+ gene sets. If none corresponds to the technology you deal |
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+ with, please choose the org.*.eg.db package according to |
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+ the organism (for example org.Hs.eg.db for Homo sapiens). |
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+ Save results of the enrichment tests in a '.rda' file |
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+ located in |
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+ \code{path}/\code{db}/\code{onto}/\code{zvalCutoff(params)}.
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+} |
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+\examples{
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+\dontrun{
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+## load an example of IcaSet |
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+data(icaSetCarbayo) |
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+ |
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+## define params |
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+# Use threshold 3 to select contributing genes. |
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+# Results of enrichment analysis will be written in path 'resPath(params)/GOstatsEnrichAnalysis' |
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+params <- buildMineICAParams(resPath="~/resMineICACarbayo/", selCutoff=3) |
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+ |
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+## Annotation package for IcaSetCarbayo is hgu133a.db. |
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+# check annotation package |
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+annotation(icaSetCarbayo) |
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+ |
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+## Define universe, i.e the set of EntrezGene IDs mapping to the feature IDs of the IcaSet object. |
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+universe <- as.character(na.omit(unique(unlist(AnnotationDbi::mget(featureNames(icaSetCarbayo), |
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+ hgu133aENTREZID, ifnotfound = NA))))) |
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+ |
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+## Apply enrichement analysis (of the contributing genes) to the first components using gene sets from KEGG. |
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+# Since an annotation package is available, we don't need to fill arg 'entrez2symbol'. |
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+# run the actual enrichment analysis |
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+hypergeoAn(icaSet=icaSetCarbayo[,,1], params=params, db="GO",onto="BP", universe=universe) |
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+} |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+\seealso{
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+ \code{\link{runEnrich}}, \code{\link[xtable]{xtable}},
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+ \code{\link[biomaRt]{useMart}},
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+ \code{\link[Category]{hyperGTest}},
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+ \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}},
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+ \code{\link{mergeGostatsResults}}
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+} |
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+ |