summary {RDAVIDWebService} | R Documentation

## Basic summary for DAVIDWebService package classes.

### Description

The different implementations of summary function for the DAVIDWebService package classes.

### Usage

      summary(object, ...)

      ## S4 method for signature 'DAVIDCluster'
    summary(object)

      ## S4 method for signature 'DAVIDGODag'
    summary(object, ...)

      ## S4 method for signature 'DAVIDWebService'
    summary(object)

### Arguments

`object` | DAVIDXX class members (where XX stands for Term/GeneCluster, GODag or DAVIDWebService).
`...` | Additional parameters.

### Value

data.frame with summary output.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### See Also

Other DAVIDCluster: `DAVIDCluster-class`, `cluster`, `cluster`, `dictionary`, `dictionary`, `enrichment`, `enrichment`, `members`, `members`, `membership`, `membership`, `subset`, `subset`

Other DAVIDGODag: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGODag-class`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `benjaminis`, `benjaminis`, `bonferronis`, `bonferronis`, `counts`, `counts`, `fdrs`, `fdrs`, `foldEnrichments`, `foldEnrichments`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `listTotals`, `listTotals`, `percentages`, `percentages`, `popHits`, `popHits`, `popTotals`, `popTotals`, `terms`, `terms`, `universeCounts`, `universeMappedCount`, `upsideDown`, `upsideDown`

Other DAVIDWebService: `DAVIDWebService-class`, `addList`, `addList`, `connect`, `connect`, `getAllAnnotationCategoryNames`, `getAllAnnotationCategoryNames`, `getAnnotationSummary`, `getAnnotationSummary`, `getBackgroundListNames`, `getBackgroundListNames`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getCurrentBackgroundListPosition`, `getCurrentBackgroundListPosition`, `getCurrentGeneListPosition`, `getCurrentGeneListPosition`, `getCurrentSpeciesPosition`, `getCurrentSpeciesPosition`, `getDefaultCategoryNames`, `getDefaultCategoryNames`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListNames`, `getGeneListNames`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getIdTypes`, `getIdTypes`, `getListName`, `getListName`, `getSpecieNames`, `getSpecieNames`, `getStub`, `getStub`, `is.connected`, `is.connected`, `setAnnotationCategories`, `setAnnotationCategories`, `setCurrentBackgroundPosition`, `setCurrentBackgroundPosition(position)`, `setCurrentGeneListPosition`, `setCurrentGeneListPosition`, `setCurrentSpecies`, `setCurrentSpecies`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`

### Examples

    {
    ##DAVIDGODag example:
    ##Load the Functional Annotation Chart file report for the input demo
    ##file 2, using data function. Then, create a DAVIDGODag object using
    ##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
    ##obtained from the loaded data.frame funChart2. In addition, we have
    ##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
    ##DAVID/GO.db database are not using the same version.
    data(funChart2)
    davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
    pvalueCutoff=0.001, removeUnattached=TRUE)
    summary(davidGODag)

    ##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
    summary(davidGeneCluster1)

    ##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
    summary(davidTermCluster2)
    }

[Package RDAVIDWebService version 1.24.0 Index]