DAVIDGeneCluster-class: class "DAVIDGeneCluster
In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description Type Extends Slots Methods Author(s) References See Also Examples

This class represents the output of a DAVID Gene Functional Classification Tool report.

This class is a "Concrete" one.

DAVIDCluster and uses its constructor to parse the report.

the ones inherited from DAVIDCluster.

initialize: signature(.Object="DAVIDGeneCluster", fileName="character"): basic cluster report file parser.
DAVIDGeneCluster: signature(fileName="character"): high level gene cluster report file parser.
ids: signature(object="DAVIDGeneCluster"): list with the member ids within each cluster.
genes: signature(object="DAVIDGeneCluster"): list with the DAVIDGenes members within each cluster.
plot2D: signature(object="DAVIDGeneCluster", color=c("FALSE"="black","TRUE"="green"), names=FALSE): ggplot2 tile plot with gene membership to each cluster.

Cristobal Fresno and Elmer A Fernandez

The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)
Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

Other DAVIDGeneCluster: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, genes, genes, genes, genes, ids, ids, ids, ids, ids, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

{
##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 the inspect the cluster with 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]]

##Then, we can obtain the ids of the members calling clusterGenes object
##which is a DAVIDGenes class or directly using ids on davidGeneCluster1.
ids(clusterGenes)
ids(davidGeneCluster1)[[higherEnrichment]]

##Obtain the genes of the first cluster using davidGeneCluster1 object.
##Or, using genes on DAVIDGenes class once we get the members of the cluster.
genes(davidGeneCluster1)[[1]]
genes(members(davidGeneCluster1)[[1]])

##Finally, we can inspect a 2D tile membership plot, to visually inspect for
##overlapping of genes across the clusters. Or use a scaled version of gene
##names to see the association of gene cluster, e.g., cluster 3 is related to
##ATP genes.
plot2D(davidGeneCluster1)
plot2D(davidGeneCluster1,names=TRUE)+
theme(axis.text.y=element_text(size=rel(0.9)))
}