R: Methods to manipulate DAVID website

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.

Examples

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

[Package RDAVIDWebService version 1.25.0 Index]