connectToBed()
after loading the package
(this function is not automatically called on package load anymore
to avoid warning message during CRAN checks)compareBedInstances()
: platform comparisonbeidsModule
and of findBeids()
interfacesfocusOnScope()
parametersis.character(metadata(BEIDList)$.lname)
dumpUniprotDb()
connectToBed()
supports the .opts parameter of RCurl::curlPerform()
.listBeIdSources()
dumpNcbiTax
: using the zip archive instead of the tar.gz because
of internal issue with firewall.convBeIds()
and getBeIdConvTable()
have an additional parameter
"canonical" to only keep canonical symbols of BE when converting from or
to symbols.dumpUniprotDb()
uses less memoryforgetBedConnection()
, dumpEnsCore()
, dumpNcbiDb()
,
dumpNcbiTax()
, dumpUniprotDb()
, getEnsemblGeneIds()
,
getEnsemblPeptideIds()
, getEnsemblTranscriptIds()
,
getNcbiGeneTransPep()
, getUniprot()
,
loadNCBIEntrezGOFunctions()
, and loadNcbiTax()
functions do not write anymore by default in the user's home file space.connectToBed()
function (by default this parameter is set to FALSE). beidsServer()
and beidsUI()
functionsfindBeids()
guessIdOrigin()
(still available) has been renamed guessIdScope()
.
It takes into account user input to guess the identifiers scope.beIDsToAllScopes()
(more specific than geneIDsToAllScopes()
)merge()
calls have been replaced by dplyr::inner_join()
.::
calls.searchBeid()
geneIDsToAllScopes()
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