DAVIDWebService-methods: Methods to manipulate DAVID website

Description Usage Arguments Details Value See Also Examples

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

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  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

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

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