Revert "Initial commit"

This reverts commit db381bb4d13f6f09a61f236f819184e5e6f43bd8.

Initial commit

Annotation for fission yeast

Delete org.Spombe.eg.sqlite

DESCRIPTION

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+Package: org.Spombe.eg.db
+Title: Genome wide annotation for Schizosaccharomyces pombe
+Description: Genome wide annotation for Schizosaccharomyces pombe, primarily based on mapping using Entrez Gene identifiers.
+Version: 0.1
+Author: Langqing Liu <[email protected]>
+Maintainer: Langqing Liu <[email protected]>
+Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.52.0)
+Suggests: DBI, annotate, RUnit
+Imports: methods, AnnotationDbi
+License: Artistic-2.0
+organism: Schizosaccharomyces pombe
+species: Schizosaccharomyces pombe
+biocViews: OrgDb, annotation
+

NAMESPACE

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+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(
+    org.Spombe.eg,
+    org.Spombe.eg_dbconn,
+    org.Spombe.eg_dbfile,
+    org.Spombe.eg_dbschema,
+    org.Spombe.eg_dbInfo,
+
+    org.Spombe.egORGANISM
+)
+

R/zzz.R

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+datacache <- new.env(hash=TRUE, parent=emptyenv())
+
+org.Spombe.eg <- function() showQCData("org.Spombe.eg", datacache)
+org.Spombe.eg_dbconn <- function() dbconn(datacache)
+org.Spombe.eg_dbfile <- function() dbfile(datacache)
+org.Spombe.eg_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices)
+org.Spombe.eg_dbInfo <- function() dbInfo(datacache)
+
+org.Spombe.egORGANISM <- "Schizosaccharomyces pombe"
+
+.onLoad <- function(libname, pkgname)
+{
+    ## Connect to the SQLite DB
+    dbfile <- system.file("extdata", "org.Spombe.eg.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)
+    db <- loadDb(system.file("extdata", paste(sPkgname,
+      ".sqlite",sep=""), package=pkgname, lib.loc=libname),
+                   packageName=pkgname)    
+    dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"OrgDb")
+    ns <- asNamespace(pkgname)
+    assign(dbNewname, db, envir=ns)
+    namespaceExport(ns, dbNewname)
+
+    packageStartupMessage(AnnotationDbi:::annoStartupMessages("org.Spombe.eg.db"))
+}
+
+.onUnload <- function(libpath)
+{
+    dbFileDisconnect(org.Spombe.eg_dbconn())
+}
+

man/org.Spombe.egBASE.Rd

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+\name{org.Spombe.eg.db}
+\alias{org.Spombe.eg.db}
+\alias{org.Spombe.eg}
+\title{Bioconductor annotation data package}
+\description{
+
+  Welcome to the org.Spombe.eg.db annotation Package.  This is an
+  organism specific package. The purpose is to provide detailed
+  information about the species abbreviated in the second part of the
+  package name org.Spombe.eg.db. This package is updated biannually.
+
+  To learn more about this package, users are encouraged to learn about
+  the select, columns, keys and keytypes methods.  These are described
+  in a walkthrough on the bioconductor website as well as in the manual
+  pages and vignettes in the AnnotationDbi package.
+}
+\keyword{datasets}
+

man/org.Spombe.egORGANISM.Rd

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+\name{org.Spombe.egORGANISM}
+\alias{org.Spombe.egORGANISM}
+\title{The Organism for org.Spombe.eg}
+\description{
+  org.Spombe.egORGANISM is an R object that contains a single item: a
+  character string that names the organism for which org.Spombe.eg was built.
+}
+
+\details{
+  Although the package name is suggestive of the organism for which it
+  was built, org.Spombe.egORGANISM provides a simple way to programmatically
+  extract the organism name.
+}
+
+\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:
+org.Spombe.egORGANISM
+}
+
+\keyword{datasets}
+

man/org.Spombe.eg_dbconn.Rd

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+
+\name{org.Spombe.eg_dbconn}
+
+\alias{org.Spombe.eg_dbconn}
+\alias{org.Spombe.eg_dbfile}
+\alias{org.Spombe.eg_dbschema}
+\alias{org.Spombe.eg_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{
+  org.Spombe.eg_dbconn()
+  org.Spombe.eg_dbfile()
+  org.Spombe.eg_dbschema(file="", show.indices=FALSE)
+  org.Spombe.eg_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{org.Spombe.eg_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{org.Spombe.eg_dbconn} or you will break all the
+  \code{\link[AnnotationDbi:AnnDbObj-class]{AnnDbObj}} objects defined
+  in this package!
+
+  \code{org.Spombe.eg_dbfile} returns the path (character string) to the
+  package annotation DB (this is an SQLite file).
+
+  \code{org.Spombe.eg_dbschema} prints the schema definition of the
+  package annotation DB.
+
+  \code{org.Spombe.eg_dbInfo} prints other information about the package
+  annotation DB.
+}
+
+\value{
+  \code{org.Spombe.eg_dbconn}: a DBIConnection object representing an
+  open connection to the package annotation DB.
+
+  \code{org.Spombe.eg_dbfile}: a character string with the path to the
+  package annotation DB.
+
+  \code{org.Spombe.eg_dbschema}: none (invisible \code{NULL}).
+
+  \code{org.Spombe.eg_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 "genes" table:
+  dbGetQuery(org.Spombe.eg_dbconn(), "SELECT COUNT(*) FROM genes")
+
+  org.Spombe.eg_dbschema()
+
+  org.Spombe.eg_dbInfo()
+}
+
+\keyword{utilities}
+\keyword{datasets}
+