DAVIDCluster-methods: Methods for 'DAVIDCluster' class object

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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  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

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{
##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]]
}

Bioconductor-mirror/RDAVIDWebService documentation built on May 31, 2017, 10:42 p.m.