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commit b69fda6f968ba4b8a34645514a5138eb23948567 Author: Andreas Tille <[email protected]> Date: Mon Oct 2 13:56:18 2017 +0200 New upstream version 3.4.0 --- DESCRIPTION | 13 +++++ NAMESPACE | 14 ++++++ R/zzz.R | 37 ++++++++++++++ debian/README.test | 5 -- debian/changelog | 13 ----- debian/compat | 1 - debian/control | 25 --------- debian/copyright | 134 ------------------------------------------------- debian/rules | 4 -- debian/source/format | 1 - debian/watch | 3 -- inst/extdata/GO.sqlite | Bin 0 -> 97032192 bytes man/GOBASE.Rd | 35 +++++++++++++ man/GOBPANCESTOR.Rd | 54 ++++++++++++++++++++ man/GOBPCHILDREN.Rd | 61 ++++++++++++++++++++++ man/GOBPOFFSPRING.Rd | 55 ++++++++++++++++++++ man/GOBPPARENTS.Rd | 66 ++++++++++++++++++++++++ man/GOCCANCESTOR.Rd | 54 ++++++++++++++++++++ man/GOCCCHILDREN.Rd | 60 ++++++++++++++++++++++ man/GOCCOFFSPRING.Rd | 54 ++++++++++++++++++++ man/GOCCPARENTS.Rd | 64 +++++++++++++++++++++++ man/GOMAPCOUNTS.Rd | 51 +++++++++++++++++++ man/GOMFANCESTOR.Rd | 55 ++++++++++++++++++++ man/GOMFCHILDREN.Rd | 60 ++++++++++++++++++++++ man/GOMFOFFSPRING.Rd | 54 ++++++++++++++++++++ man/GOMFPARENTS.Rd | 66 ++++++++++++++++++++++++ man/GOOBSOLETE.Rd | 44 ++++++++++++++++ man/GOSYNONYM.Rd | 34 +++++++++++++ man/GOTERM.Rd | 60 ++++++++++++++++++++++ man/GO_dbconn.Rd | 87 ++++++++++++++++++++++++++++++++ 30 files changed, 1078 insertions(+), 186 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..71fc253 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,13 @@ +Package: GO.db +Title: A set of annotation maps describing the entire Gene Ontology +Description: A set of annotation maps describing the entire Gene Ontology assembled using data from GO +Version: 3.4.0 +Author: Marc Carlson +Maintainer: Bioconductor Package Maintainer <[email protected]> +Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.35.4) +Imports: methods, AnnotationDbi +Suggests: DBI +License: Artistic-2.0 +biocViews: AnnotationData, FunctionalAnnotation +NeedsCompilation: no +Packaged: 2016-10-02 21:51:35 UTC; root diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..de133c2 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,14 @@ +import(methods) +import(AnnotationDbi) + +### Only put what is statically exported here. All the AnnObj instances +### created at load time are dynamically exported (refer to R/zzz.R for +### the details). +export( + GO, + GO_dbconn, + GO_dbfile, + GO_dbschema, + GO_dbInfo +) + diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..420a727 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,37 @@ +datacache <- new.env(hash=TRUE, parent=emptyenv()) + +GO <- function() showQCData("GO", datacache) +GO_dbconn <- function() dbconn(datacache) +GO_dbfile <- function() dbfile(datacache) +GO_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) +GO_dbInfo <- function() dbInfo(datacache) + +.onLoad <- function(libname, pkgname) +{ + ## Connect to the SQLite DB + dbfile <- system.file("extdata", "GO.sqlite", package=pkgname, lib.loc=libname) + assign("dbfile", dbfile, envir=datacache) + dbconn <- dbFileConnect(dbfile) + assign("dbconn", dbconn, envir=datacache) + + ## Create the OrgDb object + sPkgname <- sub(".db$","",pkgname) + txdb <- loadDb(system.file("extdata", paste(sPkgname, + ".sqlite",sep=""), package=pkgname, lib.loc=libname), + packageName=pkgname) + dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"GODb") + ns <- asNamespace(pkgname) + assign(dbNewname, txdb, envir=ns) + namespaceExport(ns, dbNewname) + + ## Create the AnnObj instances + ann_objs <- createAnnObjs.SchemaChoice("GO_DB", "GO", "GO", dbconn, datacache) + mergeToNamespaceAndExport(ann_objs, pkgname) + packageStartupMessage(AnnotationDbi:::annoStartupMessages("GO.db")) +} + +.onUnload <- function(libpath) +{ + dbFileDisconnect(GO_dbconn()) +} + diff --git a/debian/README.test b/debian/README.test deleted file mode 100644 index 149dd05..0000000 --- a/debian/README.test +++ /dev/null @@ -1,5 +0,0 @@ -Notes on how this package can be tested. -──────────────────────────────────────── - -This package can be tested by loading it into R with the command -‘library(GO.db)’ in order to confirm its integrity. diff --git a/debian/changelog b/debian/changelog deleted file mode 100644 index 53e4cbd..0000000 --- a/debian/changelog +++ /dev/null @@ -1,13 +0,0 @@ -r-bioc-go.db (3.4.0-1) unstable; urgency=medium - - * New upstream version - * Convert to dh-r - * Generic BioConductor homepage - - -- Andreas Tille <[email protected]> Fri, 28 Oct 2016 08:59:52 +0200 - -r-bioc-go.db (3.3.0-1) unstable; urgency=low - - * Initial release (closes: #824805) - - -- Andreas Tille <[email protected]> Fri, 20 May 2016 00:14:08 +0200 diff --git a/debian/compat b/debian/compat deleted file mode 100644 index ec63514..0000000 --- a/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/debian/control b/debian/control deleted file mode 100644 index 2269755..0000000 --- a/debian/control +++ /dev/null @@ -1,25 +0,0 @@ -Source: r-bioc-go.db -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> -Section: gnu-r -Priority: optional -Build-Depends: debhelper (>= 9), - dh-r, - r-base-dev, - r-bioc-annotationdbi -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-go.db/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/ -Homepage: https://bioconductor.org/packages/GO.db/ - -Package: r-bioc-go.db -Architecture: all -Depends: ${R:Depends}, - ${misc:Depends} -Recommends: ${R:Recommends} -Suggests: ${R:Suggests} -Description: annotation maps describing the entire Gene Ontology - This package is part of BioConductor and provides a set of annotation - maps describing the entire Gene Ontology assembled using data from GO. - . - The package helps running the test suites of some BioConductor packages. diff --git a/debian/copyright b/debian/copyright deleted file mode 100644 index e158644..0000000 --- a/debian/copyright +++ /dev/null @@ -1,134 +0,0 @@ -Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: GO.db -Upstream-Contact: Bioconductor Package Maintainer <[email protected]> -Source: https://bioconductor.org/packages/GO.db/ - -Files: * -Copyright: 2006-2016 Marc Carlson -License: Artistic-2.0 - -Files: debian/* -Copyright: 2016 Andreas Tille <[email protected]> -License: Artistic-2.0 - -License: Artistic-2.0 - Permission for Use and Modification Without Distribution - . - (1) You are permitted to use the Standard Version and create and use - Modified Versions for any purpose without restriction, provided that you - do not Distribute the Modified Version. Permissions for Redistribution - of the Standard Version - . - (2) You may Distribute verbatim copies of the Source form of the - Standard Version of this Package in any medium without restriction, - either gratis or for a Distributor Fee, provided that you duplicate all - of the original copyright notices and associated disclaimers. At your - discretion, such verbatim copies may or may not include a Compiled form - of the Package. - . - (3) You may apply any bug fixes, portability changes, and other - modifications made available from the Copyright Holder. The resulting - Package will still be considered the Standard Version, and as such will - be subject to the Original License. Distribution of Modified Versions - of the Package as Source - . - (4) You may Distribute your Modified Version as Source (either gratis - or for a Distributor Fee, and with or without a Compiled form of the - Modified Version) provided that you clearly document how it differs from - the Standard Version, including, but not limited to, documenting any - non-standard features, executables, or modules, and provided that you do - at least ONE of the following: - . - (a) make the Modified Version available to the Copyright Holder of - the Standard Version, under the Original License, so that the - Copyright Holder may include your modifications in the Standard - Version. - (b) ensure that installation of your Modified Version does not - prevent the user installing or running the Standard Version. In - addition, the Modified Version must bear a name that is different - from the name of the Standard Version. - (c) allow anyone who receives a copy of the Modified Version to - make the Source form of the Modified Version available to others - under - (i) the Original License or - (ii) a license that permits the licensee to freely copy, modify - and redistribute the Modified Version using the same licensing - terms that apply to the copy that the licensee received, and - requires that the Source form of the Modified Version, and of - any works derived from it, be made freely available in that - license fees are prohibited but Distributor Fees are allowed. - . - Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source - . - (5) You may Distribute Compiled forms of the Standard Version without - the Source, provided that you include complete instructions on how to - get the Source of the Standard Version. Such instructions must be valid - at the time of your distribution. If these instructions, at any time - while you are carrying out such distribution, become invalid, you must - provide new instructions on demand or cease further distribution. If you - provide valid instructions or cease distribution within thirty days - after you become aware that the instructions are invalid, then you do - not forfeit any of your rights under this license. - . - (6) You may Distribute a Modified Version in Compiled form without the - Source, provided that you comply with Section 4 with respect to the - Source of the Modified Version. - . - Aggregating or Linking the Package - . - (7) You may aggregate the Package (either the Standard Version or - Modified Version) with other packages and Distribute the resulting - aggregation provided that you do not charge a licensing fee for the - Package. Distributor Fees are permitted, and licensing fees for other - components in the aggregation are permitted. The terms of this license - apply to the use and Distribution of the Standard or Modified Versions - as included in the aggregation. - . - (8) You are permitted to link Modified and Standard Versions with other - works, to embed the Package in a larger work of your own, or to build - stand-alone binary or bytecode versions of applications that include the - Package, and Distribute the result without restriction, provided the - result does not expose a direct interface to the Package. - . - Items That are Not Considered Part of a Modified Version - . - (9) Works (including, but not limited to, modules and scripts) that - merely extend or make use of the Package, do not, by themselves, cause - the Package to be a Modified Version. In addition, such works are not - considered parts of the Package itself, and are not subject to the terms - of this license. - . - General Provisions - . - (10) Any use, modification, and distribution of the Standard or - Modified Versions is governed by this Artistic License. By using, - modifying or distributing the Package, you accept this license. Do not - use, modify, or distribute the Package, if you do not accept this - license. - . - (11) If your Modified Version has been derived from a Modified Version - made by someone other than you, you are nevertheless required to ensure - that your Modified Version complies with the requirements of this - license. - . - (12) This license does not grant you the right to use any trademark, - service mark, tradename, or logo of the Copyright Holder. - . - (13) This license includes the non-exclusive, worldwide, free-of-charge - patent license to make, have made, use, offer to sell, sell, import and - otherwise transfer the Package with respect to any patent claims - licensable by the Copyright Holder that are necessarily infringed by the - Package. If you institute patent litigation (including a cross-claim or - counterclaim) against any party alleging that the Package constitutes - direct or contributory patent infringement, then this Artistic License - to you shall terminate on the date that such litigation is filed. - . - (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT - HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED - WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A - PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT - PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER - OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR - CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, - EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/debian/rules b/debian/rules deleted file mode 100755 index 68d9a36..0000000 --- a/debian/rules +++ /dev/null @@ -1,4 +0,0 @@ -#!/usr/bin/make -f - -%: - dh $@ --buildsystem R diff --git a/debian/source/format b/debian/source/format deleted file mode 100644 index 163aaf8..0000000 --- a/debian/source/format +++ /dev/null @@ -1 +0,0 @@ -3.0 (quilt) diff --git a/debian/watch b/debian/watch deleted file mode 100644 index 4aa6006..0000000 --- a/debian/watch +++ /dev/null @@ -1,3 +0,0 @@ -version=3 -opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/data/annotation? \ - http://bioconductor.org/packages/release/data/annotation/html/GO.db.html .*/GO.db_([\d\.]+)\.tar\.gz diff --git a/inst/extdata/GO.sqlite b/inst/extdata/GO.sqlite new file mode 100644 index 0000000..172b0b0 Binary files /dev/null and b/inst/extdata/GO.sqlite differ diff --git a/man/GOBASE.Rd b/man/GOBASE.Rd new file mode 100644 index 0000000..5b2561f --- /dev/null +++ b/man/GOBASE.Rd @@ -0,0 +1,35 @@ +\name{GO.db} +\alias{GO.db} +\alias{GO} +\title{Bioconductor annotation data package} +\description{ + + Welcome to the GO.db annotation Package. The purpose of this + package is to provide detailed information about the latest version of the + Gene Ontologies. This package is updated biannually. + + Objects in this package are accessed using the \code{select()} interface. + See ?select in the AnnotationDbi package for details. +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + \code{keys()}, \code{columns()} and \code{select()}. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. +columns(GO.db) + +## Bimap interface: +## The 'old style' of interacting with these objects is manipulation as +## bimaps. While this approach is still available we strongly encourage the +## use of select(). +ls("package:GO.db") +} +\keyword{datasets} + diff --git a/man/GOBPANCESTOR.Rd b/man/GOBPANCESTOR.Rd new file mode 100644 index 0000000..ed6b23e --- /dev/null +++ b/man/GOBPANCESTOR.Rd @@ -0,0 +1,54 @@ +\name{GOBPANCESTOR} +\alias{GOBPANCESTOR} +\title{Annotation of GO Identifiers to their Biological Process Ancestors} +\description{ + This data set describes associations between GO Biological Process (BP) + terms and their ancestor BP terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO BP terms to all ancestor terms, where an + ancestor term is a more general GO term that precedes + the given GO term in the DAG (in other words, the parents, and all + their parents, etc.). +} +\details{ + Each GO BP term is mapped to a vector of ancestor GO BP terms. + + Biological process is defined as the broad biological goals, such as + mitosis or purine metabolism, that are accomplished by ordered + assemblies of molecular functions as defined by Gene Ontology + Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOBPANCESTOR) +# Remove GO IDs that do not have any ancestor +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the ancestor GO IDs for the first two elents of xx + goids <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOBPCHILDREN.Rd b/man/GOBPCHILDREN.Rd new file mode 100644 index 0000000..4826024 --- /dev/null +++ b/man/GOBPCHILDREN.Rd @@ -0,0 +1,61 @@ +\name{GOBPCHILDREN} +\alias{GOBPCHILDREN} +\title{Annotation of GO Identifiers to their Biological Process Children} +\description{ +This data set describes associations between GO molecular function (BP) + terms and their direct children BP terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO BP terms to all direct children terms, where a + direct child term is a more specific GO term that is immediately preceded + by the given GO term in the DAG. +} +\details{ + Each GO BP term is mapped to a vector of children GO BP terms. + + Biological process is defined as the broad biological goals, such as + mitosis or purine metabolism, that are accomplished by ordered + assemblies of molecular functions as defined by Gene Ontology + Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOBPCHILDREN) +# Remove GO IDs that do not have any children +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the parent GO IDs for the first elents of xx + goids <- xx[[1]] + # Find out the GO terms for the first parent goid + GOID(GOTERM[[goids[1]]]) + Term(GOTERM[[goids[1]]]) + Synonym(GOTERM[[goids[1]]]) + Secondary(GOTERM[[goids[1]]]) + Definition(GOTERM[[goids[1]]]) + Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOBPOFFSPRING.Rd b/man/GOBPOFFSPRING.Rd new file mode 100644 index 0000000..0eac23a --- /dev/null +++ b/man/GOBPOFFSPRING.Rd @@ -0,0 +1,55 @@ +\name{GOBPOFFSPRING} +\alias{GOBPOFFSPRING} +\title{Annotation of GO Identifiers to their Biological Process Offspring} +\description{ + This data set describes associations between GO molecular function (BP) + terms and their offspring BP terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO BP terms to all offspring terms, where an + offspring term is a more specific GO term that is preceded + by the given GO term in the DAG (in other words, the children and all + their children, etc.). +} + +\details{ + Each GO BP term is mapped to a vector of offspring GO BP terms. + + Biological process is defined as the broad biological goals, such as + mitosis or purine metabolism, that are accomplished by ordered + assemblies of molecular functions as defined by Gene Ontology + Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOBPOFFSPRING) +# Remove GO IDs that do not have any offspring +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the offspring GO IDs for the first two elents of xx + goids <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOBPPARENTS.Rd b/man/GOBPPARENTS.Rd new file mode 100644 index 0000000..30abf9f --- /dev/null +++ b/man/GOBPPARENTS.Rd @@ -0,0 +1,66 @@ +\name{GOBPPARENTS} +\alias{GOBPPARENTS} +\title{Annotation of GO Identifiers to their Biological Process Parents} +\description{ + This data set describes associations between GO molecular function (BP) + terms and their direct parent BP terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO BP terms to all direct parent terms, where a + direct parent term is a more general GO term that immediately precedes + the given GO term in the DAG. +} +\details{ + Each GO BP term is mapped to a named vector of GO BP terms. The name + associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof}, + where \emph{isa} indicates that the child term is a more specific version + of the parent, and \emph{hasa} and \emph{partof} indicate that the + child term is a part of the parent. For example, a telomere is part of + a chromosome. + + Biological process is defined as the broad biological goals, such as + mitosis or purine metabolism, that are accomplished by ordered + assemblies of molecular functions as defined by Gene Ontology + Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOBPPARENTS) +# Remove GO IDs that do not have any parent +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the children GO IDs for the first elents of xx + goids <- xx[[1]] + # Find out the GO terms for the first parent goid + GOID(GOTERM[[goids[1]]]) + Term(GOTERM[[goids[1]]]) + Synonym(GOTERM[[goids[1]]]) + Secondary(GOTERM[[goids[1]]]) + Definition(GOTERM[[goids[1]]]) + Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOCCANCESTOR.Rd b/man/GOCCANCESTOR.Rd new file mode 100644 index 0000000..c446c6b --- /dev/null +++ b/man/GOCCANCESTOR.Rd @@ -0,0 +1,54 @@ +\name{GOCCANCESTOR} +\alias{GOCCANCESTOR} +\title{Annotation of GO Identifiers to their Cellular Component Ancestors} +\description{ + This data set describes associations between GO molecular function (CC) + terms and their ancestor CC terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO CC terms to all ancestor terms, where an + ancestor term is a more general GO term that precedes + the given GO term in the DAG (in other words, the parents, and all + their parents, etc.). +} +\details{ + Each GO CC term is mapped to a vector of ancestor GO C terms. + + Cellular component is defined as the subcellular structures, + locations, and macromolecular complexes; examples include nucleus, + telomere, and origin recognition complex as defined by Gene Ontology + Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOCCANCESTOR) +# Remove GO IDs that do not have any ancestor +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the ancestor GO IDs for the first two elents of xx + goids <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOCCCHILDREN.Rd b/man/GOCCCHILDREN.Rd new file mode 100644 index 0000000..398eb50 --- /dev/null +++ b/man/GOCCCHILDREN.Rd @@ -0,0 +1,60 @@ +\name{GOCCCHILDREN} +\alias{GOCCCHILDREN} +\title{Annotation of GO Identifiers to their Cellular Component Children} +\description{ + This data set describes associations between GO molecular function (CC) + terms and their direct children CC terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO CC terms to all direct children terms, where a + direct child term is a more specific GO term that is immediately preceded + by the given GO term in the DAG. +} +\details{ + Each GO CC term is mapped to a vector of children GO CC terms. + + Cellular component is defined as the subcellular structures, + locations, and macromolecular complexes; examples include nucleus, + telomere, and origin recognition complex as defined by Gene Ontology + Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOCCCHILDREN) +# Remove GO IDs that do not have any children +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ +goids <- xx[[1]] +# Find out the GO terms for the first parent goid +GOID(GOTERM[[goids[1]]]) +Term(GOTERM[[goids[1]]]) +Synonym(GOTERM[[goids[1]]]) +Secondary(GOTERM[[goids[1]]]) +Definition(GOTERM[[goids[1]]]) +Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOCCOFFSPRING.Rd b/man/GOCCOFFSPRING.Rd new file mode 100644 index 0000000..3e745d2 --- /dev/null +++ b/man/GOCCOFFSPRING.Rd @@ -0,0 +1,54 @@ +\name{GOCCOFFSPRING} +\alias{GOCCOFFSPRING} +\title{Annotation of GO Identifiers to their Cellular Component Offspring} +\description{ + This data set describes associations between GO molecular function (MF) + terms and their offspring MF terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO MF terms to all offspring terms, where an + offspring term is a more specific GO term that is preceded + by the given GO term in the DAG (in other words, the children and all + their children, etc.). +} +\details{ + Each GO CC term is mapped to a vector of offspring GO MF terms. + + Cellular component is defined as the subcellular structures, + locations, and macromolecular complexes; examples include nucleus, + telomere, and origin recognition complex as defined b y Gene Ontology + Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOCCOFFSPRING) +# Remove GO identifiers that do not have any offspring +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the offspring GO identifiers for the first two elents of xx + goidentifiers <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOCCPARENTS.Rd b/man/GOCCPARENTS.Rd new file mode 100644 index 0000000..c7c7a1e --- /dev/null +++ b/man/GOCCPARENTS.Rd @@ -0,0 +1,64 @@ +\name{GOCCPARENTS} +\alias{GOCCPARENTS} +\title{Annotation of GO Identifiers to their Cellular Component Parents} +\description{ + This data set describes associations between GO molecular function (CC) + terms and their direct parent CC terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO CC terms to all direct parent terms, where a + direct parent term is a more general GO term that immediately precedes + the given GO term in the DAG. +} +\details{ + Each GO CC term is mapped to a named vector of GO CC terms. The name + associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof}, + where \emph{isa} indicates that the child term is a more specific version + of the parent, and \emph{hasa} and \emph{partof} indicate that the + child term is a part of the parent. For example, a telomere is part of + a chromosome. + + Cellular component is defined as the subcellular structures, + locations, and macromolecular complexes; examples include nucleus, + telomere, and origin recognition complex as defined b y Gene Ontology + Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOCCPARENTS) +# Remove GO IDs that do not have any parent +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + goids <- xx[[1]] + # Find out the GO terms for the first parent go ID + GOID(GOTERM[[goids[1]]]) + Term(GOTERM[[goids[1]]]) + Synonym(GOTERM[[goids[1]]]) + Secondary(GOTERM[[goids[1]]]) + Definition(GOTERM[[goids[1]]]) + Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOMAPCOUNTS.Rd b/man/GOMAPCOUNTS.Rd new file mode 100644 index 0000000..0c8218e --- /dev/null +++ b/man/GOMAPCOUNTS.Rd @@ -0,0 +1,51 @@ +\name{GOMAPCOUNTS} + +\alias{GOMAPCOUNTS} + + +\title{Number of mapped keys for the maps in package GO.db} + +\description{ + GOMAPCOUNTS provides the "map count" (i.e. the + count of mapped keys) for each map in package GO.db. +} + +\details{ + This "map count" information is precalculated and stored in the + package annotation DB. This allows some quality control and is used by + the \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}} + function defined in AnnotationDbi to compare and validate different + methods (like \code{count.mappedkeys(x)} or + \code{sum(!is.na(as.list(x)))}) for getting the "map count" of a given + map. +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}}, + \item \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}}, + \item \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}} + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +GOMAPCOUNTS +mapnames <- names(GOMAPCOUNTS) +GOMAPCOUNTS[mapnames[1]] +x <- get(mapnames[1]) +sum(!is.na(as.list(x))) +count.mappedkeys(x) # much faster! + +## Check the "map count" of all the maps in package GO.db +checkMAPCOUNTS("GO.db") +} + +\keyword{datasets} + diff --git a/man/GOMFANCESTOR.Rd b/man/GOMFANCESTOR.Rd new file mode 100644 index 0000000..825dfd5 --- /dev/null +++ b/man/GOMFANCESTOR.Rd @@ -0,0 +1,55 @@ +\name{GOMFANCESTOR} +\alias{GOMFANCESTOR} +\title{Annotation of GO identifiers to their Molecular Function Ancestors} +\description{ + This data set describes associations between GO molecular function (MF) + terms and their ancestor MF terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO MF terms to all ancestor terms, where an + ancestor term is a more general GO term that precedes + the given GO term in the DAG (in other words, the parents, and all + their parents, etc.). +} + +\details{ + Each GO MF term is mapped to a vector of ancestor GO MF terms. + + Molecular function is defined as the tasks performed by individual + gene products; examples are transcription factor and DNA helicase as + defined by Gene Ontology Consortium. + + Mappings were based on data provided: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOMFANCESTOR) +# Remove GO identifiers that do not have any ancestor +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the ancestor GO identifiers for the first two elents of xx + goids <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOMFCHILDREN.Rd b/man/GOMFCHILDREN.Rd new file mode 100644 index 0000000..00d8b1f --- /dev/null +++ b/man/GOMFCHILDREN.Rd @@ -0,0 +1,60 @@ +\name{GOMFCHILDREN} +\alias{GOMFCHILDREN} +\title{Annotation of GO Identifiers to their Molecular Function Children} +\description{ + This data set describes associations between GO molecular function (MF) + terms and their direct children MF terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO MF terms to all direct children terms, where a + direct child term is a more specific GO term that is immediately preceded + by the given GO term in the DAG. +} +\details{ + Each GO MF term is mapped to a vector of children GO MF terms. + + Molecular function is defined as the tasks performed by individual + gene products; examples are transcription factor and DNA helicase as + defined by Gene Ontology Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOMFCHILDREN) +# Remove GO identifiers that do not have any children +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the children GO identifiers for the first elents of xx + goids <- xx[[1]] + # Find out the GO terms for the first parent goid + GOID(GOTERM[[goids[1]]]) + Term(GOTERM[[goids[1]]]) + Synonym(GOTERM[[goids[1]]]) + Secondary(GOTERM[[goids[1]]]) + Definition(GOTERM[[goids[1]]]) + Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOMFOFFSPRING.Rd b/man/GOMFOFFSPRING.Rd new file mode 100644 index 0000000..09fa05d --- /dev/null +++ b/man/GOMFOFFSPRING.Rd @@ -0,0 +1,54 @@ +\name{GOMFOFFSPRING} +\alias{GOMFOFFSPRING} +\title{Annotation of GO Identifiers to their Molecular Function Offspring} +\description{ + This data set describes associations between GO molecular function (MF) + terms and their offspring MF terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO MF terms to all offspring terms, where an + offspring term is a more specific GO term that is preceded + by the given GO term in the DAG (in other words, the children and all + their children, etc.). +} +\details{ + Each GO MF term is mapped to a vector of offspring GO MF terms. + + Molecular function is defined as the tasks performed by individual + gene products; examples are transcription factor and DNA helicase as + defined by Gene Ontology Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ +\url{http://www.geneontology.org/} and +\url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOMFOFFSPRING) +# Remove GO identifiers that do not have any offspring +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the offspring GO identifiers for the first two elents of xx +goids <- xx[1:2] +} +} +\keyword{datasets} + diff --git a/man/GOMFPARENTS.Rd b/man/GOMFPARENTS.Rd new file mode 100644 index 0000000..ebd7a35 --- /dev/null +++ b/man/GOMFPARENTS.Rd @@ -0,0 +1,66 @@ +\name{GOMFPARENTS} +\alias{GOMFPARENTS} +\title{Annotation of GO Identifiers to their Molecular Function Parents} +\description{ + This data set describes associations between GO molecular function (MF) + terms and their direct parent MF terms, based on the directed acyclic + graph (DAG) defined by the Gene Ontology Consortium. The format is an R + object mapping the GO MF terms to all direct parent terms, where a + direct parent term is a more general GO term that immediately precedes + the given GO term in the DAG. +} + +\details{ + Each GO MF term is mapped to a named vector of GO MF terms. The name + associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof}, + where \emph{isa} indicates that the child term is a more specific version + of the parent, and \emph{hasa} and \emph{partof} indicate that the + child term is a part of the parent. For example, a telomere is part of + a chromosome. + + Molecular function is defined as the tasks performed by individual + gene products; examples are transcription factor and DNA helicase as + defined by the Gene Ontology Consortium. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} + +\references{ + \url{http://www.geneontology.org/} and + \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOMFPARENTS) +# Remove GO identifiers that do not have any parent +xx <- xx[!is.na(xx)] +if(length(xx) > 0){ + # Get the parent GO identifiers for the first elents of xx + goids <- xx[[1]] + # Find out the GO terms for the first parent goid + GOID(GOTERM[[goids[1]]]) + Term(GOTERM[[goids[1]]]) + Synonym(GOTERM[[goids[1]]]) + Secondary(GOTERM[[goids[1]]]) + Definition(GOTERM[[goids[1]]]) + Ontology(GOTERM[[goids[1]]]) +} +} +\keyword{datasets} + diff --git a/man/GOOBSOLETE.Rd b/man/GOOBSOLETE.Rd new file mode 100644 index 0000000..6de9774 --- /dev/null +++ b/man/GOOBSOLETE.Rd @@ -0,0 +1,44 @@ +\name{GOOBSOLETE} +\alias{GOOBSOLETE} +\title{Annotation of GO identifiers by terms defined by Gene Ontology + Consortium and their status are obsolete} +\description{ +This is an R object mapping GO identifiers to the specific +terms in defined by Gene Ontology Consortium and their definition are obsolete +} +\details{ + All the obsolete GO terms that are collected in this index will no longer exist + in other mapping objects. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} +\references{ + \url{https://www.ncib.nlm.nih.gov/LocusLink} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOTERM) +if(length(xx) > 0){ + # Get the TERMS for the first elent of xx + GOID(xx[[1]]) + Ontology(xx[[1]]) +} +} +\keyword{datasets} + diff --git a/man/GOSYNONYM.Rd b/man/GOSYNONYM.Rd new file mode 100644 index 0000000..cbb10ca --- /dev/null +++ b/man/GOSYNONYM.Rd @@ -0,0 +1,34 @@ +\name{GOSYNONYM} +\alias{GOSYNONYM} +\title{Map from GO synonyms to GO terms} +\description{ + GOSYNONYM is an R object that provides mapping + from GO synonyms to GO terms +} + +\details{ + [TODO: Put some details here] +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +x <- GOSYNONYM +sample(x, 3) +# GO ID "GO:0009435" has a lot of synonyms +GOTERM[["GO:0009435"]] +# GO ID "GO:0006736" is a synonym of GO ID "GO:0009435" +GOID(GOSYNONYM[["GO:0006736"]]) +} +\keyword{datasets} + diff --git a/man/GOTERM.Rd b/man/GOTERM.Rd new file mode 100644 index 0000000..2158484 --- /dev/null +++ b/man/GOTERM.Rd @@ -0,0 +1,60 @@ +\name{GOTERM} +\alias{GOTERM} +\title{Annotation of GO Identifiers to GO Terms} +\description{ + This data set gives mappings between GO identifiers and their respective terms. +} +\details{ + Each GO identifier is mapped to a \code{GOTerms} object that has 6 slots: + GOID: GO Identifier + Term: The term for that GO id + Synonym: Synonymous terms + Secondary: Secondary terms that have been merged into this term + Definition: Further definition of the GO term + Ontology: One of MF - molecular function, BP - biological + process, or CC - cellular component + + All the obsolete GO terms are under the nodes "obsolete molecular + function" (GO:0008369), "obsolete cellular component" (GO id + GO:0008370), and "obsolete biological process" (GO:0008371). Each of + these GO identifiers has a group of GO identifiers as their direct children with GO + terms that were defined by GO but are + deprecated in the current build. These deprecated GO terms were + appended by "(obsolete)" when the data package was built. + + Mappings were based on data provided by: Gene Ontology + ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ + With a date stamp from the source of: 2016-Sep21 + +} +\references{ + \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} +} + +\seealso{ + \itemize{ + \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of + the \code{select()} interface. + } +} + +\examples{ +## select() interface: +## Objects in this package can be accessed using the select() interface +## from the AnnotationDbi package. See ?select for details. + +## Bimap interface: +# Convert the object to a list +xx <- as.list(GOTERM) +if(length(xx) > 0){ + # Get the TERMS for the first elent of xx + GOID(xx[[1]]) + Term(xx[[1]]) + Synonym(xx[[1]]) + Secondary(xx[[1]]) + Definition(xx[[1]]) + Ontology(xx[[1]]) +} +} +\keyword{datasets} + diff --git a/man/GO_dbconn.Rd b/man/GO_dbconn.Rd new file mode 100644 index 0000000..1d27cc1 --- /dev/null +++ b/man/GO_dbconn.Rd @@ -0,0 +1,87 @@ + +\name{GO_dbconn} + +\alias{GO_dbconn} +\alias{GO_dbfile} +\alias{GO_dbschema} +\alias{GO_dbInfo} + + +\title{Collect information about the package annotation DB} + +\description{ + Some convenience functions for getting a connection object to (or collecting + information about) the package annotation DB. +} + +\usage{ + GO_dbconn() + GO_dbfile() + GO_dbschema(file="", show.indices=FALSE) + GO_dbInfo() +} + +\arguments{ + \item{file}{ + A connection, or a character string naming the file to print to (see + the \code{file} argument of the \code{\link[base]{cat}} function for + the details). + } + \item{show.indices}{ + The CREATE INDEX statements are not shown by default. + Use \code{show.indices=TRUE} to get them. + } +} + +\details{ + \code{GO_dbconn} returns a connection object to the + package annotation DB. IMPORTANT: Don't call + \code{\link[DBI:dbConnect]{dbDisconnect}} on the connection object + returned by \code{GO_dbconn} or you will break all the + \code{\link[AnnotationDbi:AnnDbObj-class]{AnnDbObj}} objects defined + in this package! + + \code{GO_dbfile} returns the path (character string) to the + package annotation DB (this is an SQLite file). + + \code{GO_dbschema} prints the schema definition of the + package annotation DB. + + \code{GO_dbInfo} prints other information about the package + annotation DB. +} + +\value{ + \code{GO_dbconn}: a DBIConnection object representing an + open connection to the package annotation DB. + + \code{GO_dbfile}: a character string with the path to the + package annotation DB. + + \code{GO_dbschema}: none (invisible \code{NULL}). + + \code{GO_dbInfo}: none (invisible \code{NULL}). +} + +\seealso{ + \code{\link[DBI:dbSendQuery]{dbGetQuery}}, + \code{\link[DBI:dbConnect]{dbConnect}}, + \code{\link[AnnotationDbi:AnnDbObj-class]{dbconn}}, + \code{\link[AnnotationDbi:AnnDbObj-class]{dbfile}}, + \code{\link[AnnotationDbi:AnnDbObj-class]{dbschema}}, + \code{\link[AnnotationDbi:AnnDbObj-class]{dbInfo}} +} + +\examples{ + library(DBI) + ## Count the number of rows in the "go_term" table: + dbGetQuery(GO_dbconn(), "SELECT COUNT(*) FROM go_term") + + GO_dbschema() + + GO_dbInfo() +} + +\keyword{utilities} +\keyword{datasets} + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-go.db.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
