{
##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)
##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/geneListReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidGenes1<-DAVIDGenes(untar(fileName,list=TRUE))
##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.
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)
##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/functionalAnnotationChartReport2.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidFunChart2<-DAVIDFunctionalAnnotationChart(untar(fileName, list=TRUE))
##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)
##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/annotationTableReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidFunTable1<-DAVIDFunctionalAnnotationTable(untar(fileName, list=TRUE))
##Example DAVIDGODag
##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)
##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))
##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))
}
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