The FunctionalEnrichment
class
Source: R/AllClasses.R
, R/show-methods.R
FunctionalEnrichment-class.Rd
This class introduces the possibility to store the results of functional
enrichment analyses such as over-representation analysis (ORA), gene set
enrichment analysis (GSEA), and competitive gene set test accounting for
inter-gene correlation (CAMERA). The different slots contained in this class
are used to store enrichment results generated through the enrichGenes()
function.
Usage
# S4 method for class 'FunctionalEnrichment'
enrichmentResults(object)
# S4 method for class 'FunctionalEnrichment'
enrichmentDatabase(object)
# S4 method for class 'FunctionalEnrichment'
enrichmentMethod(object)
# S4 method for class 'FunctionalEnrichment'
geneSet(object)
# S4 method for class 'FunctionalEnrichment'
enrichmentMetric(object)
# S4 method for class 'FunctionalEnrichment'
enrichedFeatures(object)
# S4 method for class 'FunctionalEnrichment'
show(object)
Value
the
enrichmentResults()
function returns adata.frame
object with the results of the functional enrichment analysis.
the
enrichmentDatabase()
function returns acharacter
that specifies the database that provided the gene-set collection.
the
enrichmentMethod()
function returns acharacter
with the enrichment method used for the analysis.
the
geneSet()
function returns alist
with the gene-set collections retrieved.
the
enrichmentMetric()
function returns anumeric
object with ranked gene statistic used for GSEA.
the
enrichmentMetric()
function returns acharacter
object with the names of the ranked features used for GSEA.
Functions
enrichmentResults(FunctionalEnrichment)
: Access thedata
slot to take a closer look at all the enriched terms of an enrichment analysisenrichmentDatabase(FunctionalEnrichment)
: See the database used for the functional enrichmentenrichmentMethod(FunctionalEnrichment)
: Visualize the approach used for the functional enrichment analysisgeneSet(FunctionalEnrichment)
: Access thegeneSet
slot to see the collection of gene sets used for GSEAenrichmentMetric(FunctionalEnrichment)
: View the ranking metric used for GSEAenrichedFeatures(FunctionalEnrichment)
: View the names of the pre-ranked features used for GSEAshow(FunctionalEnrichment)
: Show method for objects of class FunctionalEnrichment
Slots
data
A
data.frame
object holding the output of enrichment analysismethod
The method used to perform functional enrichment analysis (e.g.
Gene Set Enrichment Analysis (GSEA)
)organism
The name of the organism under consideration (e.g.
Homo sapiens
)database
The name of the database used for the enrichment analysis (e.g.
KEGG
)pCutoff
A
numeric
value defining the threshold used for statistical significance in the enrichment analysis (e.g.0.05
)pAdjustment
A
character
indicating the method used to correct p-values for multiple testing (e.g.fdr
)features
A
character
vector containing the list of features used for the enrichmentstatistic
A
numeric
vector containing the statistic used to run GSEA. This parameter is empty for ORA and CAMERAuniverse
The background universe of features. Typically, this is equal to the complete list of features assayed. This slot is NULL for GSEA
geneSet
The gene set used for the functional enrichment analysis. It is a
list
object where each element contains the list of genes belonging to a specific pathway.
Author
Jacopo Ronchi, jacopo.ronchi@unimib.it