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]] }