/usr/lib/R/site-library/Biobase/NAMESPACE is in r-bioc-biobase 2.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | useDynLib(Biobase, copyEnv_sym=copyEnv, sublist_extract)
import(methods)
exportClasses(aggregator, container, eSet, phenoData,
MIAxE, MIAME, characterORMIAME,
annotatedDataset, AssayData, data.frameOrNULL,
exprSet, AnnotatedDataFrame,
Versions, VersionsNull, Versioned, VersionedBiobase,
ExpressionSet, MultiSet, SnpSet, NChannelSet,
ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric,
ScalarCharacter)
exportMethods("[", "[[", "$", abstract, aggenv, aggfun,
annotatedDataFrameFrom, annotation,
channel, channelNames, coerce,
combine, content, contents, description, dims, eList,
experimentData, expinfo, exprs,
featureNames, featureData, fData, fvarLabels, fvarMetadata,
geneNames, getExpData,
hybridizations, initfun,
length, locked, makeDataPackage, normControls, notes, otherInfo, pData,
phenoData, preproc, protocolData, sampleNames, samples, se.exprs,
selectChannels, snpCall, snpCallProbability, storageMode,
varLabels, varMetadata,
"annotation<-", "description<-", "dimLabels<-", "eList<-",
"experimentData<-", "exprs<-",
"featureNames<-", "featureData<-", "fData<-", "fvarLabels<-", "fvarMetadata<-",
"geneNames<-", "notes<-", "preproc<-", "pData<-",
"phenoData<-", "protocolData<-", "sampleNames<-",
"snpCall<-", "snpCallProbability<-", "varLabels<-",
"varMetadata<-", "assayData<-", "se.exprs<-", "storageMode<-",
"write.exprs", dim, dimLabels, assayData, reporterNames, "reporterNames<-",
pubMedIds, "pubMedIds<-",
isVersioned, isCurrent, classVersion, "classVersion<-",
updateObject, updateObjectTo,
initialize, show, Compare,
"counts", "counts<-",
"design", "design<-",
"dispTable", "dispTable<-",
"sizeFactors", "sizeFactors<-",
"conditions", "conditions<-",
"estimateSizeFactors",
"estimateDispersions",
"AnnotatedDataFrame",
"ExpressionSet")
export("Aggregate",
"addVigs2WinMenu",
"anyMissing",
"as.data.frame.ExpressionSet",
"assayDataNew", "assayDataValidMembers",
assayDataElementNames,
assayDataElement, assayDataElementReplace, "assayDataElement<-",
"biocReposList", "cache", "copyEnv", "copySubstitute", "getObjectSlots",
"createPackage", "df2pD", "dumpPackTxt", "esApply",
"getPkgVigs", "isUnique", "l2e", "listLen", "matchpt", "mkScalar",
"multiassign", "note", "openPDF","openVignette", "package.version",
"reverseSplit", "rowMax", "rowMedians", "rowMin", "rowQ",
read.exprSet, read.phenoData, read.pD,
readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME,
"selectSome", "strbreak", "subListExtract", "testBioCConnection",
"lcSuffix", "lcPrefix", "lcPrefixC",
"updateOldESet", "updateObjectFromSlots", "userQuery", "validMsg")
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