DAVIDClasses-genes: 'genes' for the different DAVIDWebService package class...

Description Usage Arguments Value Author(s) See Also Examples

Description

Obtain genes related information, according to the given function call (see Values).

Usage

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  genes(object, ...)

  ## S4 method for signature 'DAVIDGenes'
genes(object,ids)

  ## S4 method for signature 'DAVIDGeneCluster'
genes(object)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
genes(object,
  ...)

Arguments

object

DAVIDGenes or DAVIDGeneCluster class object.

ids

character vector with the ids to fetch.

...

Additional parameters for internal functions (if applicable).

Value

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, ...).

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

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

Examples

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{
##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]])
}

Bioconductor-mirror/RDAVIDWebService documentation built on May 31, 2017, 10:42 p.m.