genes {RDAVIDWebService} | R Documentation |
genes
for the different DAVIDWebService package class objects.Obtain genes related information, according to the given function call (see Values).
genes(object, ...) ## S4 method for signature 'DAVIDGenes' genes(object,ids) ## S4 method for signature 'DAVIDGeneCluster' genes(object) ## S4 method for signature 'DAVIDFunctionalAnnotationTable' genes(object, ...)
object |
DAVIDGenes or DAVIDGeneCluster class object. |
ids |
character vector with the ids to fetch. |
... |
Additional parameters for internal functions (if applicable). |
according to the call one of the following objects can be returned
DAVIDGenes |
a DAVIDGenes object with the matched genes of ids parameter. If missing, returns all the genes. |
DAVIDGeneCluster |
list with DAVIDGenes objects for each cluster. |
DAVIDFunctionalAnnotationTable |
a DAVIDGenes objects, according to ... parameter used internally on genes(DAVIDGenes, ...). |
Cristobal Fresno and Elmer A Fernandez
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
, dictionary
,
dictionary
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
membership
, membership
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
,
subset
, subset
Other DAVIDGeneCluster:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
,
DAVIDGeneCluster-class
,
DAVIDGenes
, DAVIDGenes
,
DAVIDGenes
, DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
, ids
,
ids
, ids
, ids
,
ids
, 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
, ids
,
ids
, ids
, ids
,
ids
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
{ ##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. data(geneList1) davidGenes1<-DAVIDGenes(geneList1) ##Now, get the genes using the ids look up parameter with the first ##six ids. If ids omitted, all the available are returned. genes(davidGenes1, ids=head(ids(davidGenes1))) ##DAVIDFunctionalAnnotationTable example: ##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) ##Now we can obtain the genes for the given ids, or the complete list if the ##parameter is omitted. genes(davidFunTable1, id=c("37166_at","41703_r_at")) ##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)) ##Then, we can obtain the genes of the first cluster using davidGeneCluster1 ##object. Or, using genes on DAVIDGenes class once we get the members of the ##cluster genes(davidGeneCluster1)[[1]] genes(members(davidGeneCluster1)[[1]]) }