ids {RDAVIDWebService} | R Documentation

## `ids` for the different DAVIDWebService package class objects

### Description

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

### Usage

      ids(object)

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

      ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
    ids(object)

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

      ## S4 method for signature 'DAVIDTermCluster'
    ids(object)

### Arguments

`object` | DAVIDWebService class object. Possible values are: DAVIDGenes, DAVIDFunctionalAnnotationChart, DAVIDGeneCluster or DAVIDTermCluster.

### Value

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

`DAVIDGenes` | character vector with gene submitted ids.
`DAVIDFunctionalAnnotationChart` | list with character/integer vector of ids of the corresponding "Category".
`DAVIDGeneCluster, DAVIDTermCluster` | list with character/integer vector of ids of the members of each cluster.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### See Also

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

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

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

### 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. Once, the report is loaded, we can retrieve the ids.
    data(geneList1)
    davidGenes1<-DAVIDGenes(geneList1)
    ids(davidGenes1)

    ##DAVIDFunctionalAnnotationChart example:
    ##Load the Functional Annotation Chart file report for the input demo
    ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
    ##object using the loaded data.frame funChart2. Once the report is loaded,
    ##the user can obtain the ids of the genes present in each Term, as a list of
    ##character vector.
    data(funChart2)
    davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)
    ids(davidFunChart2)

    ##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))
    davidGeneCluster1

    ##Now we can invoke DAVIDCluster ancestor functions to inspect the report
    ##data, of each cluster. For example, we can call summary to get a general
    ##idea, and the inspect the cluster with higher Enrichment Score, to see
    ##which members belong to it, etc. Or simply returning the whole cluster as
    ##a list with EnrichmentScore and Members.
    summary(davidGeneCluster1)
    higherEnrichment<-which.max(enrichment(davidGeneCluster1))
    clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]]
    wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]]

    ##Now, we can obtain the ids of the  first cluster directly using
    ##davidGeneCluster1 or by using DAVIDGenes class on the same cluster.
    ids(davidGeneCluster1)[[1]]
    ids(members(davidGeneCluster1)[[1]])

    ##DAVIDTermCluster example:
    ##Load the Gene Functional Classification Tool file report for the
    ##input demo file 2 to create a DAVIDGeneCluster object.
    setwd(tempdir())
    fileName<-system.file("files/termClusterReport2.tab.tar.gz",
    package="RDAVIDWebService")
    untar(fileName)
    davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
    davidTermCluster2

    ##Now we can invoke DAVIDCluster ancestor functions to inspect the report
    ##data, of each cluster. For example, we can call summary to get a general
    ##idea, and the inspect the cluster with higher Enrichment Score, to see
    ##which members belong to it, etc. Or simply returning the whole cluster as a
    ##list with EnrichmentScore and Members.
    summary(davidTermCluster2)
    higherEnrichment<-which.max(enrichment(davidTermCluster2))
    clusterGenes<-members(davidTermCluster2)[[higherEnrichment]]
    wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]]

    ##Then, we can obtain the ids of the term members calling clusterGenes object
    ##which is a DAVIDFunctionalAnnotationChart class or directly using ids on
    ##davidTermCluster2 for the higherEnrichment cluster.
    ids(clusterGenes)
    ids(davidTermCluster2)[[higherEnrichment]]
    }

[Package RDAVIDWebService version 1.24.0 Index]