DAVIDTermCluster-class {RDAVIDWebService} | R Documentation

## class "DAVIDTermCluster

### Description

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

### Type

This class is a "`Concrete`" one.

### Extends

- DAVIDCluster and uses its constructor to parse the report.

### 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

    {
    ##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)
    }

[Package RDAVIDWebService version 1.26.0 Index]