is.connected {RDAVIDWebService} | R Documentation |
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).
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)
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" |
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".
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) |
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. |
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
david <- DAVIDWebService$new() david$is.connected() ##Or the equivalent S4 style function call is.connected(david)