/usr/lib/R/site-library/AnnotationDbi/NAMESPACE is in r-bioc-annotationdbi 1.26.1-1.
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 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 | import(methods)
import(utils)
import(Biobase)
import(DBI)
import(RSQLite)
import(BiocGenerics)
importFrom(IRanges, metadata, isTRUEorFALSE, isSingleString, elementLengths)
importFrom(GenomeInfoDb, genomeStyles, extractSeqlevels, mapSeqlevels)
exportClasses(
## from R/AllClasses.R
"Bimap",
"FlatBimap",
"AnnObj",
"AnnDbObj",
#"AnnDbTable",
"L2Rlink",
"AnnDbBimap",
"GoAnnDbBimap",
"Go3AnnDbBimap",
"GOTermsAnnDbBimap",
"AnnDbMap",
"IpiAnnDbMap",
"AgiAnnDbMap",
"ProbeAnnDbBimap",
"ProbeAnnDbMap",
"ProbeIpiAnnDbMap",
"ProbeGo3AnnDbBimap",
## Virtual mother-class for all Annoations
"AnnotationDb",
"OrgDb",
"ChipDb",
"InparanoidDb",
"GODb",
"ReactomeDb",
## ## Class for faux-bimaps (select based bimaps)
## "AnnotationDbMap",
## from R/GOTerms.R
"GOTerms",
## Special Frame objects
"GOFrame",
"GOAllFrame",
"KEGGFrame"
)
exportMethods(
## from R/AnnDbObj-lowAPI.R
"dbconn",
"dbfile",
"dbmeta",
"dbschema",
"dbInfo",
#"Ltablename", "Rtablename",
#"Lfilter", "Rfilter",
#"flatten",
## from R/Bimap.R (the Bimap interface)
"direction", "direction<-",
"revmap",
"colnames", "colmetanames",
"Lkeyname", "Rkeyname", "keyname",
"tagname",
"Rattribnames", "Rattribnames<-",
"Lkeys", "Rkeys", "keys",
"Lkeys<-", "Rkeys<-", "keys<-",
"subset",
"[",
"Llength", "Rlength", "length",
"isNA",
"mappedLkeys", "mappedRkeys", "mappedkeys",
"count.mappedLkeys", "count.mappedRkeys", "count.mappedkeys",
"show",
"summary",
"toTable","as.data.frame",
"head", "tail",
"nrow",
"links",
"count.links",
"nhit",
"ncol", "dim",
"toggleProbes",
"hasMultiProbes","hasSingleProbes",
"getBimapFilters","setInpBimapFilter",
## from R/GOTerms.R
"GOID",
"Term",
"Ontology",
"Synonym",
"Secondary",
"Definition",
## Special Frame Methods
"GOFrame",
"GOAllFrame",
"getGOFrameData",
"KEGGFrame",
"getKEGGFrameData",
## from R/BimapFormatting.R
"as.list",
#"toLList", "toRList", "toList",
"as.character",
## from R/Bimap-envirAPI.R
"ls",
"mget",
"eapply",
"get",
"exists",
"[[",
"$",
"contents",
"sample",
## more...
"initialize",
##Methods for AnnotationDb
"saveDb",
"loadDb",
"species",
"columns",
"keytypes",
"select"
)
export(
unlist2,
## from R/AnnDbObj-lowAPI.R
showQCData,
## from R/SQL.R
debugSQL,
## from R/GOTerms.R
GOTerms,
makeGOGraph,
## from R/AnnDbPkg-templates-common.R
dbFileConnect,
dbFileDisconnect,
#addToNamespaceAndExport,
mergeToNamespaceAndExport,
## from the R/createAnnObjs.*_DB.R files
createAnnObjs.SchemaChoice,
## from R/AnnDbPkg-checker.R
#checkProperty0,
checkMAPCOUNTS,
## helpers for map creation, temporary
## until pluggable maps come online
make_eg_to_go_map,
make_go_to_eg_map,
toSQLStringSet,
#Convenience function to allow automatic mapping of IDs:
inpIDMapper,
intraIDMapper,
idConverter,
#Needs to be exported from RSQLite
summary,
## AnnotationDb
metadata,
## seqnames.db
supportedSeqnameMappings,
findSequenceRenamingMaps,
supportedSeqnameStyles,
extractSeqnameSet,
testSeqnames,
isSupportedSeqnamesStyle,
listAllSupportedStylesBySpecies,
listAllSupportedSeqnameStyles,
supportedSeqnames,
species,
cols ## just for deprecating cols everywhere - remove after 2.13 release
)
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