DAVIDClasses-summary: Basic summary for DAVIDWebService package classes.

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

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)
}

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.