subset {RDAVIDWebService} | R Documentation |
DAVIDFunctionalAnnotationTable
class objectObtain DAVIDFunctionalAnnotationTable related information, according to the given function call (see Values).
subset(x, ...) ## S4 method for signature 'DAVIDFunctionalAnnotationTable' subset(x,selection=c("Membership", "Dictionary"), category, drop=TRUE) dictionary(object, ...) ## S4 method for signature 'DAVIDFunctionalAnnotationTable' dictionary(object, ...) membership(object, ...) ## S4 method for signature 'DAVIDFunctionalAnnotationTable' membership(object, ...)
object,x |
DAVIDFunctionalAnnotationTable class object. |
selection |
which slot to use to obtain the subset. Possible values are "Membership" or "Dictionary". |
category |
named list with main annotation category, which contains a character vector with the ids to use. Default value is missing in order to use all available categories of the report. |
drop |
Should list structure be drop if length==1? Default value TRUE. |
... |
Additional parameters for subset function call. |
according to the call one of the following objects can be returned
subset |
list with filtered categories/ids according to function call. |
enrichment |
numeric vector with DAVID cluster's enrichment score. |
members |
list with DAVID Cluster's members. |
Cristobal Fresno and Elmer A Fernandez
Other DAVIDCluster: DAVIDCluster-class
,
cluster
, cluster
,
enrichment
, enrichment
,
members
, members
,
summary
, summary
,
summary
, summary
Other DAVIDFunctionalAnnotationTable:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable-class
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
,
categories
, categories
,
categories
, genes
,
genes
, genes
,
genes
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
Other DAVIDFunctionalAnnotationTable:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable-class
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
,
categories
, categories
,
categories
, genes
,
genes
, genes
,
genes
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
{ ##Load the Functional Annotation Table file report for the input demo ##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable ##object using the loaded data.frame annotationTable1. data(annotationTable1) davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1) ##Obtain the head of the dictionary and the membership matrix for the first ##annotated genes used in davidFunTable1 object. head(membership(davidFunTable1, categories(davidFunTable1)[1])) head(dictionary(davidFunTable1, categories(davidFunTable1)[1])) head(genes(davidFunTable1)) }