R: Methods for 'DAVIDFunctionalAnnotationTable' class object

subset {RDAVIDWebService}

R Documentation

Methods for `DAVIDFunctionalAnnotationTable` class object

Description

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

Usage

  subset(x, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
subset(x,selection=c("Membership",
  "Dictionary"), category, drop=TRUE)

  dictionary(object, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
dictionary(object,
  ...)

  membership(object, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
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.

Author(s)

Cristobal Fresno and Elmer A Fernandez

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))
}

[Package RDAVIDWebService version 1.25.0 Index]

Methods for DAVIDFunctionalAnnotationTable class object