ids {RDAVIDWebService} | R Documentation |
ids
for the different DAVIDWebService package class objectsObtain ids related information, according to the given function call (see Values).
ids(object) ## S4 method for signature 'DAVIDGenes' ids(object) ## S4 method for signature 'DAVIDFunctionalAnnotationChart' ids(object) ## S4 method for signature 'DAVIDGeneCluster' ids(object) ## S4 method for signature 'DAVIDTermCluster' ids(object)
object |
DAVIDWebService class object. Possible values are: DAVIDGenes, DAVIDFunctionalAnnotationChart, DAVIDGeneCluster or DAVIDTermCluster. |
according to the call one of the following objects can be returned
DAVIDGenes |
character vector with gene submitted ids. |
DAVIDFunctionalAnnotationChart |
list with character/integer vector of ids of the corresponding "Category". |
DAVIDGeneCluster,
DAVIDTermCluster |
list with character/integer vector of ids of the members of each cluster. |
Cristobal Fresno and Elmer A Fernandez
Other DAVIDFunctionalAnnotationChart:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart-class
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
,
categories
, categories
,
categories
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
Other DAVIDGeneCluster:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
,
DAVIDGeneCluster-class
,
DAVIDGenes
, DAVIDGenes
,
DAVIDGenes
, DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
, genes
,
genes
, genes
,
genes
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
Other DAVIDGenes:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDGenes-class
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
, genes
,
genes
, genes
,
genes
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
Other DAVIDTermCluster:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
,
DAVIDTermCluster-class
, as
,
as
, as
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
{ ##DAVIDGenes example: ##Load Show Gene List file report for the input demo file 1, using data ##function. Then, create a DAVIDGenes object using the loaded data.frame ##geneList1. Once, the report is loaded, we can retrieve the ids. data(geneList1) davidGenes1<-DAVIDGenes(geneList1) ids(davidGenes1) ##DAVIDFunctionalAnnotationChart example: ##Load the Functional Annotation Chart file report for the input demo ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart ##object using the loaded data.frame funChart2. Once the report is loaded, ##the user can obtain the ids of the genes present in each Term, as a list of ##character vector. data(funChart2) davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2) ids(davidFunChart2) ##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, 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(davidGeneCluster1) higherEnrichment<-which.max(enrichment(davidGeneCluster1)) clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]] wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]] ##Now, we can obtain the ids of the first cluster directly using ##davidGeneCluster1 or by using DAVIDGenes class on the same cluster. ids(davidGeneCluster1)[[1]] ids(members(davidGeneCluster1)[[1]]) ##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, 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]] }