DAVIDTermCluster-class: class "DAVIDTermCluster

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

Description

This class represents the output of a DAVID Functional Annotation Clustering report.

Type

This class is a "Concrete" one.

Extends

Slots

the ones inherited from DAVIDCluster.

Methods

initialize

signature(.Object="DAVIDTermCluster", fileName="character"): basic cluster report file parser.

DAVIDTermCluster

signature(fileName="character"): high level gene cluster report file parser.

ids

signature(object="DAVIDTermCluster"): list with the member ids within each cluster.

plot2D

signature(object="DAVIDTermCluster", number=1, color=c("FALSE"="black","TRUE"="green")): ggplot2 tile plot of genes vs functional annotation category membership of the given cluster number.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

  1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

  2. 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

See Also

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

Examples

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{
##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 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(davidTermCluster2)
higherEnrichment<-which.max(enrichment(davidTermCluster2))
clusterGenes<-members(davidTermCluster2)[[higherEnrichment]]
wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]]

##Then, we can obtain the ids of the term members calling clusterGenes object
##which is a DAVIDFunctionalAnnotationChart class or directly using ids on
##davidTermCluster2 for the higherEnrichment cluster.
ids(clusterGenes)
ids(davidTermCluster2)[[higherEnrichment]]

##Finally, we can inspect a 2D tile membership plot, to visual inspect for
##overlapping of genes across the term members of the selected cluster.
plot2D(davidTermCluster2, number=higherEnrichment)
}

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