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

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))
}

[Package RDAVIDWebService version 1.18.0 Index]