RDAVIDWebService (version 1.10.0)

subset: Methods for DAVIDFunctionalAnnotationTable class object

Description

Obtain DAVIDFunctionalAnnotationTable related information, according to the given function call (see Values).

Usage

subset(x, ...)
  "subset"(x,selection=c("Membership", "Dictionary"), category, drop=TRUE)
  dictionary(object, ...)
  "dictionary"(object, ...)
  membership(object, ...)
  "membership"(object, ...)

Arguments

object,x

DAVIDFunctionalAnnotationTable class object.

selection

which slot to use to obtain the subset. Possible values are "Membership" or "Dictionary".

category

named list with main annotation category, which contains a character vector with the ids to use. Default value is missing in order to use all available categories of the report.

drop

Should list structure be drop if length==1? Default value TRUE.

...

Additional parameters for subset function call.

Value

according to the call one of the following objects can be returned

subset

list with filtered categories/ids according to function call.

enrichment

numeric vector with DAVID cluster's enrichment score.

members

list with DAVID Cluster's members.

See Also

Other DAVIDCluster: DAVIDCluster-class, cluster, cluster, enrichment, enrichment, members, members, summary, summary, summary, summary

Other DAVIDFunctionalAnnotationTable: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable-class, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, categories, categories, categories, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Other DAVIDFunctionalAnnotationTable: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable-class, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, categories, categories, categories, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Examples

{
##Load the Functional Annotation Table file report for the input demo
##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
##object using the loaded data.frame annotationTable1.
data(annotationTable1)
davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)

##Obtain the head of the dictionary and the membership matrix for the first
##annotated genes used in davidFunTable1 object.
head(membership(davidFunTable1, categories(davidFunTable1)[1]))
head(dictionary(davidFunTable1, categories(davidFunTable1)[1]))
head(genes(davidFunTable1))
}