RDAVIDWebService (version 1.10.0)

cluster: Methods for DAVIDCluster class object

Description

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

Usage

cluster(object)
  "cluster"(object)
  enrichment(object)
  "enrichment"(object)
  members(object)
  "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.

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]]
}