hypergeoAn | R Documentation |
GOstats
.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
.
hypergeoAn(icaSet, params,
path = paste(resPath(params), "GOstatsEnrichAnalysis/", sep = "/"),
SlistSel, hgCutoff = 0.01, db = "go", onto = "BP",
cond = TRUE, universe, entrez2symbol)
icaSet |
An object of class |
params |
An object of class
|
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 ( |
onto |
A character specifying the GO ontology to
use. Must be one of |
cond |
A logical indicating whether the calculation
should conditioned on the GO structure, see
|
universe |
The universe for the hypergeometric
tests, see
|
entrez2symbol |
A vector of all gene Symbols
involved in the analysis indexed by their Entrez Gene
IDs. It is only used when |
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)
.
Anne Biton
runEnrich
, xtable
,
useMart
,
hyperGTest
,
GOHyperGParams
,
mergeGostatsResults
## 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)
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