summary {RDAVIDWebService} | R Documentation |
The different implementations of summary function for the DAVIDWebService package classes.
summary(object, ...) ## S4 method for signature 'DAVIDCluster' summary(object) ## S4 method for signature 'DAVIDGODag' summary(object, ...) ## S4 method for signature 'DAVIDWebService' summary(object)
object |
DAVIDXX class members (where XX stands for Term/GeneCluster, GODag or DAVIDWebService). |
... |
Additional parameters. |
data.frame with summary output.
Cristobal Fresno and Elmer A Fernandez
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
{ ##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) }