hypergeoAn: Runs an enrichment analysis per component using package...

Description Usage Arguments Details Author(s) See Also Examples

View source: R/functions_enrich.R

Description

Runs an enrichment analysis of the contributing genes associated with each component, using the function hyperGTest of package GOstats. The easiest way to run enrichment analysis is to use function runEnrich.

Usage

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  hypergeoAn(icaSet, params,
    path = paste(resPath(params), "GOstatsEnrichAnalysis/", sep = "/"),
    SlistSel, hgCutoff = 0.01, db = "go", onto = "BP",
    cond = TRUE, universe, entrez2symbol)

Arguments

icaSet

An object of class IcaSet

params

An object of class MineICAParams containing the parameters of the analysis

path

The path where results will be saved

SlistSel

A list of contributing gene projection values per component. Each element of the list corresponds to a component and is restricted to the features or genes exceeding a given threshold. If missing, is computed by the function.

hgCutoff

The p-value threshold

db

The database to be used ("GO" or "KEGG")

onto

A character specifying the GO ontology to use. Must be one of "BP", "CC", or "MF", see GOHyperGParams. Only used when argument db is "GO".

cond

A logical indicating whether the calculation should conditioned on the GO structure, see GOHyperGParams.

universe

The universe for the hypergeometric tests, see GOHyperGParams.

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.

Details

An annotation package must be available in annotation(icaSet) to provide the contents of the gene sets. If none corresponds to the technology you deal with, please choose the org.*.eg.db package according to the organism (for example org.Hs.eg.db for Homo sapiens). Save results of the enrichment tests in a '.rda' file located in path/db/onto/zvalCutoff(params).

Author(s)

Anne Biton

See Also

runEnrich, xtable, useMart, hyperGTest, GOHyperGParams, mergeGostatsResults

Examples

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## Not run: 
## load an example of IcaSet
data(icaSetCarbayo)

## define params
# Use threshold 3 to select contributing genes.
# Results of enrichment analysis will be written in path 'resPath(params)/GOstatsEnrichAnalysis'
params <- buildMineICAParams(resPath="~/resMineICACarbayo/", selCutoff=3)

## Annotation package for IcaSetCarbayo is hgu133a.db.
# check annotation package
annotation(icaSetCarbayo)

## Define universe, i.e the set of EntrezGene IDs mapping to the feature IDs of the IcaSet object.
universe <- as.character(na.omit(unique(unlist(AnnotationDbi::mget(featureNames(icaSetCarbayo),
                         hgu133aENTREZID, ifnotfound = NA)))))

## Apply enrichement analysis (of the contributing genes) to the first components using gene sets from KEGG.
# Since an annotation package is available, we don't need to fill arg 'entrez2symbol'.
# run the actual enrichment analysis
hypergeoAn(icaSet=icaSetCarbayo[,,1], params=params, db="GO",onto="BP", universe=universe)

## End(Not run)

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