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)
"is.connected"(object)
connect(object)
"connect"(object)
getIdTypes(object)
"getIdTypes"(object)
addList(object, inputIds, idType, listName, listType=c("Gene", "Background"))
"addList"(object, inputIds, idType, listName, listType=c("Gene", "Background"))
getAllAnnotationCategoryNames(object)
"getAllAnnotationCategoryNames"(object)
getDefaultCategoryNames(object)
"getDefaultCategoryNames"(object)
getGeneListNames(object)
"getGeneListNames"(object)
getBackgroundListNames(object)
"getBackgroundListNames"(object)
getListName(object, listType=c("Gene", "Background"), position=1L)
"getListName"(object, listType=c("Gene", "Background"), position=1L)
getSpecieNames(object)
"getSpecieNames"(object)
getCurrentGeneListPosition(object)
"getCurrentGeneListPosition"(object)
getCurrentBackgroundListPosition(object)
"getCurrentBackgroundListPosition"(object)
getCurrentSpeciesPosition(object)
"getCurrentSpeciesPosition"(object)
getTimeOut(object)
"getTimeOut"(object)
getHttpProtocolVersion(object)
"getHttpProtocolVersion"(object)
setCurrentGeneListPosition(object, position)
"setCurrentGeneListPosition"(object, position)
setCurrentBackgroundPosition(object, position)
"setCurrentBackgroundPosition"(object, position)
setCurrentSpecies(object, species)
"setCurrentSpecies"(object, species)
setAnnotationCategories(object, categories)
"setAnnotationCategories"(object, categories)
setTimeOut(object, milliSeconds)
"setTimeOut"(object, milliSeconds)
setHttpProtocolVersion(object, version)
"setHttpProtocolVersion"(object, version)
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.connect
:
is.connected
:getIdTypes
:addList
:
getAllAnnotationCategoryNames
:
getDefaultCategoryNames
:
getGeneListNames
:
getBackgroundListNames
:getListName
:
getSpecieNames
:
getCurrentGeneListPosition
:
getCurrentBackgroundListPosition
:
getCurrentSpeciesPosition
:
setCurrentGeneListPosition
:
setCurrentBackgroundPosition:
setCurrentSpecies
:
setAnnotationCategories
:getTimeOut
:
setTimeOut
:
getHttpProtocolVersion
:
setHttpProtocolVersion
: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)
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