is.connected {RDAVIDWebService} | R Documentation

## Methods to manipulate DAVID website

### Description

`DAVIDWebService` class methods to manipulate DAVID website status from R. This includes different functionalities to set up and track the connexion, upload a Gene/Background list, check the species, etc. Note that `DAVIDWebService` is a Reference class, hence invoke it using object_name$method_name(parameters). In addition, the user can use the S4 version style function call (see Details).

### Usage

      is.connected(object)

      ## S4 method for signature 'DAVIDWebService'
    is.connected(object)

      connect(object)

      ## S4 method for signature 'DAVIDWebService'
    connect(object)

      getIdTypes(object)

      ## S4 method for signature 'DAVIDWebService'
    getIdTypes(object)

      addList(object, inputIds, idType, listName,
      listType=c("Gene", "Background"))

      ## S4 method for signature 'DAVIDWebService'
    addList(object, inputIds,
      idType, listName, listType=c("Gene", "Background"))

      getAllAnnotationCategoryNames(object)

      ## S4 method for signature 'DAVIDWebService'
    getAllAnnotationCategoryNames(object)

      getDefaultCategoryNames(object)

      ## S4 method for signature 'DAVIDWebService'
    getDefaultCategoryNames(object)

      getGeneListNames(object)

      ## S4 method for signature 'DAVIDWebService'
    getGeneListNames(object)

      getBackgroundListNames(object)

      ## S4 method for signature 'DAVIDWebService'
    getBackgroundListNames(object)

      getListName(object, listType=c("Gene", "Background"),
      position=1L)

      ## S4 method for signature 'DAVIDWebService'
    getListName(object,
      listType=c("Gene", "Background"), position=1L)

      getSpecieNames(object)

      ## S4 method for signature 'DAVIDWebService'
    getSpecieNames(object)

      getCurrentGeneListPosition(object)

      ## S4 method for signature 'DAVIDWebService'
    getCurrentGeneListPosition(object)

      getCurrentBackgroundListPosition(object)

      ## S4 method for signature 'DAVIDWebService'
    getCurrentBackgroundListPosition(object)

      getCurrentSpeciesPosition(object)

      ## S4 method for signature 'DAVIDWebService'
    getCurrentSpeciesPosition(object)

      getTimeOut(object)

      ## S4 method for signature 'DAVIDWebService'
    getTimeOut(object)

      getHttpProtocolVersion(object)

      ## S4 method for signature 'DAVIDWebService'
    getHttpProtocolVersion(object)

      setCurrentGeneListPosition(object, position)

      ## S4 method for signature 'DAVIDWebService'
    setCurrentGeneListPosition(object,
      position)

      setCurrentBackgroundPosition(object, position)

      ## S4 method for signature 'DAVIDWebService'
    setCurrentBackgroundPosition(object,
      position)

      setCurrentSpecies(object, species)

      ## S4 method for signature 'DAVIDWebService'
    setCurrentSpecies(object,
      species)

      setAnnotationCategories(object, categories)

      ## S4 method for signature 'DAVIDWebService'
    setAnnotationCategories(object,
      categories)

      setTimeOut(object, milliSeconds)

      ## S4 method for signature 'DAVIDWebService'
    setTimeOut(object, milliSeconds)

      setHttpProtocolVersion(object, version)

      ## S4 method for signature 'DAVIDWebService'
    setHttpProtocolVersion(object, version)

### Arguments

`object` | DAVIDWebService class object.
`inputIds` | character vector with the associated ids.
`idType` | character with the type of submitted ids.
`listName` | character to identify the submitted list.
`listType` | character with the type of list (Gene, Background). Default value is "Gene".
`position` | integer with the position of the gene/background list to set.
`species` | numeric vector with the specie/s to use.
`categories` | character vector with the category name/s to use in the analysis.
`milliSeconds` | integer with time defined in milli seconds.
`version` | character with HTTP_PROTOCOL_VERSION to use. At present available strings are: "1.1", "1.0", "HTTP/1.1" and "HTTP/1.0"

### Details

Available functions include:

`connect`:

  Try to establish a connection with DAVID server using the provided email.

`is.connected`:

  Check if connected to DAVID server.

`getIdTypes`:

  Returns all acceptable DAVID idTypes.

`addList`:

  Add a gene or background to the current session.

`getAllAnnotationCategoryNames`:

  Returns all available annotation category names.

`getDefaultCategoryNames`:

  Returns all default category names.

`getGeneListNames`:

  Returns all list names

`getBackgroundListNames`:

  Returns background names.

`getListName`:

  Get the name of the selected list type at a given position.

`getSpecieNames`:

  Return specie/s of the current gene list.

`getCurrentGeneListPosition`:

  Return the position of current gene list.

`getCurrentBackgroundListPosition`:

  Return the position of current background list.

`getCurrentSpeciesPosition`:

  Return current specie/s used positions for the uploaded gene list.

`setCurrentGeneListPosition`:

  Use the gene list of the given position.

`setCurrentBackgroundPosition:`

  Use the background list of the given position.

`setCurrentSpecies`:

  Select the specie/s of the submitted gene list to use in the analysis.

`setAnnotationCategories`:

  Let the user to select specific annotation categories.

`getTimeOut`:

  Get apache Axis time out in milliSeconds.

`setTimeOut`:

  Set apache Axis time out in milliSeconds.

`getHttpProtocolVersion`:

  Get apache Axis HTTP_PROTOCOL_VERSION.

`setHttpProtocolVersion`:

  Set apache Axis HTTP_PROTOCOL_VERSION. possible values are defined in org.apache.axis2.transport.http.HTTPConstants class with HEADER_PROTOCOL_XX property. At present available strings are: "1.1", "1.0", "HTTP/1.1" and "HTTP/1.0".

### Value

according to the call one of the following objects can be returned

`is.connected` | TRUE if user has registered email with DAVID knowledge base, FALSE otherwise.
`getIdTypes` | character vector with the available DAVID input ID type.
`addList` | list with two items: i)`inDavid`, a numeric with the percentage of the inputIds in DAVID knowledge database, ii)`unmappedIds`, a character vector with the unmapped ids if listType is "Gene", NA_character_ otherwise.
`getAllAnnotationCategoryNames` | character vector with the available DAVID annotation categories.
`getDefaultCategoryNames` | character vector with a subset of the available DAVID annotation categories, chosen by default.
`getGeneListNames` | return a character vector with the name of the submitted gene list/s.
`getBackgroundListNames` | character vector with the name of the available background gene list/s for the submitted gene list/s.
`getListName` | character with the name of the list.
`getSpecieNames` | character vector with the specie/s and in brackets the number of DAVID Ids of the current gene list, e.g. Homo sapiens(155).
`getCurrentGeneListPosition` | integer with the position of current gene list if available, NA_integer_ otherwise.
`getCurrentBackgroundListPosition` | integer with the position of current background list if available, NA_integer_ otherwise.
`getCurrentSpeciesPosition` | integer vector with the specie/s position under use for the gene list under use if available, NA_character_ otherwise.

### See Also

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

Other DAVIDWebService: `DAVIDWebService-class`, `getAnnotationSummary`, `getAnnotationSummary`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getStub`, `getStub`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

### Examples

    david <- DAVIDWebService$new()
    david$is.connected()
    ##Or the equivalent S4 style function call
    is.connected(david)

[Package RDAVIDWebService version 1.18.0 Index]