| cluster {RDAVIDWebService} | R Documentation |
DAVIDCluster class objectObtain DAVIDCluster related information, according to the given function call (see Values).
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)
object |
DAVIDCluster class object. |
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. |
Cristobal Fresno and Elmer A Fernandez
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
{
##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]]
}