cluster {RDAVIDWebService} | R Documentation

## Methods for `DAVIDCluster` class object

### Description

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

### Usage

      cluster(object)

      ## S4 method for signature 'DAVIDCluster'
    cluster(object)

      enrichment(object)

      ## S4 method for signature 'DAVIDCluster'
    enrichment(object)

      members(object)

      ## S4 method for signature 'DAVIDCluster'
    members(object)

### Arguments

`object` | DAVIDCluster class object.

### Value

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

`cluster` | list with DAVIDCluster object slot.
`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`, `dictionary`, `dictionary`, `membership`, `membership`, `subset`, `subset`, `summary`, `summary`, `summary`, `summary`

Other DAVIDCluster: `DAVIDCluster-class`, `dictionary`, `dictionary`, `membership`, `membership`, `subset`, `subset`, `summary`, `summary`, `summary`, `summary`

Other DAVIDCluster: `DAVIDCluster-class`, `dictionary`, `dictionary`, `membership`, `membership`, `subset`, `subset`, `summary`, `summary`, `summary`, `summary`

### Examples

    {
    ##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 then inspect the cluster with the 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]]

    ##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 then inspect the cluster with the 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]]
    }

[Package RDAVIDWebService version 1.18.0 Index]