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]