DAVIDGenes {RDAVIDWebService} | R Documentation

## High level constructors for DAVIDWebService package's classes.

### Description

Different ways to build the different DAVIDWebService's object according to the signature in use.

### Usage

      DAVIDGenes(object)

      ## S4 method for signature 'character'
    DAVIDGenes(object)

      ## S4 method for signature 'data.frame'
    DAVIDGenes(object)

      ## S4 method for signature 'DAVIDGenes'
    initialize(.Object, fileName)

      as(object, Class, strict=TRUE,
      ext=possibleExtends(thisClass, Class))

      DAVIDFunctionalAnnotationChart(object)

      ## S4 method for signature 'character'
    DAVIDFunctionalAnnotationChart(object)

      ## S4 method for signature 'data.frame'
    DAVIDFunctionalAnnotationChart(object)

      ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
    initialize(.Object,
      fileName)

      as(object, Class, strict=TRUE,
      ext=possibleExtends(thisClass, Class))

      ## S4 method for signature 'DAVIDCluster'
    initialize(.Object, fileName)

      ## S4 method for signature 'DAVIDGeneCluster'
    initialize(.Object,
      fileName)

      DAVIDGeneCluster(object)

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

      ## S4 method for signature 'DAVIDTermCluster'
    initialize(.Object,
      fileName)

      DAVIDTermCluster(object)

      ## S4 method for signature 'character'
    DAVIDTermCluster(object)

      ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
    initialize(.Object,
      fileName)

      as(object, Class, strict=TRUE,
      ext=possibleExtends(thisClass, Class))

      DAVIDFunctionalAnnotationTable(object)

      ## S4 method for signature 'character'
    DAVIDFunctionalAnnotationTable(object)

      ## S4 method for signature 'data.frame'
    DAVIDFunctionalAnnotationTable(object)

      ## S4 method for signature 'DAVIDGODag'
    initialize(.Object,funChart,type=c("BP","MF","CC"),pvalueCutoff=0.1,removeUnattached=FALSE,...)

      DAVIDGODag(funChart, ...)

      ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
    DAVIDGODag(funChart,
      ...)

### Arguments

`object` | could be a character with the file name of the .tab report or data.frame already loaded.
`fileName` | character with the file name of the .tab report to load.
`.Object` | character to use in new function call. Possible values are: "DAVIDGenes", "DAVIDFunctionalAnnotationChart" or "DAVIDCluster".
`Class` | character to use in the `as` function call. Possible values are: "DAVIDGenes" and "DAVIDFunctionalAnnotationChart".
`strict,ext` | see `as` function.
`funChart` | DAVIDFunctionalAnnotationChart object.
`type` | character to indicate Gene Ontology main category: "BP", "MF" or "CC".
`pvalueCutoff` | numeric >0 <=1 to indicate the p-value to use as the threshold for enrichment. Default value is 0.1
`removeUnattached` | Should unattached nodes be removed from GO DAG? Default value is FALSE.
`...` | Additional parameters for lower level constructors (initialize).

### Value

a DAVIDWebService object according to function call:

`DAVIDGenes` | object with genes description related data.
`DAVIDFunctionalAnnotationChart` | object with the respective report.
`DAVIDFunctionalAnnotationTable` | object with the respective report.
`DAVIDCluster` | Not possible to invoke as it is a Virtual class.
`DAVIDGeneCluster` | object with the respective report.
`DAVIDTermCluster` | object with the respective report.
`DAVIDGODag` | derived GOstats GO Direct Acyclic Graph from DAVIDFunctionalAnnotationChart data.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### See Also

Other DAVIDFunctionalAnnotationChart: `DAVIDFunctionalAnnotationChart-class`, `categories`, `categories`, `categories`, `ids`, `ids`, `ids`, `ids`, `ids`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`

Other DAVIDFunctionalAnnotationTable: `DAVIDFunctionalAnnotationTable-class`, `categories`, `categories`, `categories`, `dictionary`, `dictionary`, `genes`, `genes`, `genes`, `genes`, `membership`, `membership`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `subset`, `subset`

Other DAVIDGODag: `DAVIDGODag-class`, `benjaminis`, `benjaminis`, `bonferronis`, `bonferronis`, `counts`, `counts`, `fdrs`, `fdrs`, `foldEnrichments`, `foldEnrichments`, `listTotals`, `listTotals`, `percentages`, `percentages`, `popHits`, `popHits`, `popTotals`, `popTotals`, `summary`, `summary`, `summary`, `summary`, `terms`, `terms`, `universeCounts`, `universeMappedCount`, `upsideDown`, `upsideDown`

Other DAVIDGeneCluster: `DAVIDGeneCluster-class`, `genes`, `genes`, `genes`, `genes`, `ids`, `ids`, `ids`, `ids`, `ids`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`

Other DAVIDGenes: `DAVIDGenes-class`, `genes`, `genes`, `genes`, `genes`, `ids`, `ids`, `ids`, `ids`, `ids`

Other DAVIDTermCluster: `DAVIDTermCluster-class`, `ids`, `ids`, `ids`, `ids`, `ids`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`

### Examples

    {
    ##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))
    }

[Package RDAVIDWebService version 1.24.0 Index]