genes {RDAVIDWebService} | R Documentation

## `genes` for the different DAVIDWebService package class objects.

### Description

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

### Usage

      genes(object, ...)

      ## S4 method for signature 'DAVIDGenes'
    genes(object,ids)

      ## S4 method for signature 'DAVIDGeneCluster'
    genes(object)

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

### Arguments

`object` | DAVIDGenes or DAVIDGeneCluster class object.
`ids` | character vector with the ids to fetch.
`...` | Additional parameters for internal functions (if applicable).

### Value

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

`DAVIDGenes` | a DAVIDGenes object with the matched genes of ids parameter. If missing, returns all the genes.
`DAVIDGeneCluster` | list with DAVIDGenes objects for each cluster.
`DAVIDFunctionalAnnotationTable` | a DAVIDGenes objects, according to ... parameter used internally on genes(DAVIDGenes, ...).

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### See Also

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`, `dictionary`, `dictionary`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `membership`, `membership`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `subset`, `subset`

Other DAVIDGeneCluster: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGeneCluster-class`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`

Other DAVIDGenes: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes-class`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`

### Examples

    {
    ##DAVIDGenes example:
    ##Load Show Gene List file report for the input demo file 1, using data
    ##function. Then, create a DAVIDGenes object using the loaded data.frame
    ##geneList1.
    data(geneList1)
    davidGenes1<-DAVIDGenes(geneList1)

    ##Now, get the genes using the ids look up parameter with the first
    ##six ids. If ids omitted, all the available are returned.
    genes(davidGenes1, ids=head(ids(davidGenes1)))

    ##DAVIDFunctionalAnnotationTable example:
    ##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)

    ##Now we can obtain the genes for the given ids, or the complete list if the
    ##parameter is omitted.
    genes(davidFunTable1, id=c("37166_at","41703_r_at"))

    ##DAVIDGeneCluster example:
    ##Load the Gene Functional Classification Tool file report for the
    ##input demo list 1 file to create a DAVIDGeneCluster object.
    setwd(tempdir())
    fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
    package="RDAVIDWebService")
    untar(fileName)
    davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))

    ##Then, we can obtain the genes of the first cluster using davidGeneCluster1
    ##object. Or, using genes on DAVIDGenes class once we get the members of the
    ##cluster
    genes(davidGeneCluster1)[[1]]
    genes(members(davidGeneCluster1)[[1]])
    }

[Package RDAVIDWebService version 1.18.0 Index]