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\name{AnnDbObj-objects}
\docType{class}
\alias{AnnDbObj-objects}
% Classes
\alias{AnnDbObj}
\alias{class:AnnDbObj}
\alias{AnnDbObj-class}
% Accessor-like methods
\alias{dbconn}
\alias{dbconn,SQLiteConnection-method}
\alias{dbconn,environment-method}
\alias{dbconn,AnnDbObj-method}
\alias{dbfile}
\alias{dbfile,SQLiteConnection-method}
\alias{dbfile,environment-method}
\alias{dbfile,AnnDbObj-method}
\alias{dbmeta}
\alias{dbmeta,DBIConnection-method}
\alias{dbmeta,environment-method}
\alias{dbmeta,AnnDbObj-method}
\alias{dbschema}
\alias{dbschema,DBIConnection-method}
\alias{dbschema,environment-method}
\alias{dbschema,AnnDbObj-method}
\alias{dbInfo}
\alias{dbInfo,DBIConnection-method}
\alias{dbInfo,environment-method}
\alias{dbInfo,AnnDbObj-method}
\title{AnnDbObj objects}
\description{
The AnnDbObj class is the most general container for storing any kind
of SQLite-based annotation data.
}
\details{
Many classes in AnnotationDbi inherit directly or indirectly
from the AnnDbObj class. One important particular case is the
\link{AnnDbBimap} class which is the lowest class in the AnnDbObj
hierarchy to also inherit the \link{Bimap} interface.
}
\section{Accessor-like methods}{
In the code snippets below,
\code{x} is an AnnDbObj object.
\describe{
\item{}{
\code{dbconn(x)}:
Return a connection object to the SQLite DB containing \code{x}'s data.
}
}
\describe{
\item{}{
\code{dbfile(x)}:
Return the path (character string) to the SQLite DB (file) containing
\code{x}'s data.
}
}
\describe{
\item{}{
\code{dbmeta(x, name)}:
Print the value of metadata whose name is 'name'.
Also works if \code{x} is a DBIConnection object.
}
}
\describe{
\item{}{
\code{dbschema(x, file="", show.indices=FALSE)}:
Print the schema definition of the SQLite DB.
Also works if \code{x} is a DBIConnection object.
The \code{file} argument must be a connection, or a character string
naming the file to print to (see the \code{file} argument of the
\code{\link[base:cat]{cat}} function for the details).
The CREATE INDEX statements are not shown by default.
Use \code{show.indices=TRUE} to get them.
}
}
\describe{
\item{}{
\code{dbInfo(x)}:
Prints other information about the SQLite DB.
Also works if \code{x} is a DBIConnection object.
}
}
}
\seealso{
\code{\link[DBI:dbConnect]{dbConnect}},
\code{\link[DBI:dbListTables]{dbListTables}},
\code{\link[DBI:dbListTables]{dbListFields}},
\code{\link[DBI:dbSendQuery]{dbGetQuery}},
\link{Bimap}
}
\examples{
library("hgu95av2.db")
dbconn(hgu95av2ENTREZID) # same as hgu95av2_dbconn()
dbfile(hgu95av2ENTREZID) # same as hgu95av2_dbfile()
dbmeta(hgu95av2_dbconn(), "ORGANISM")
dbmeta(hgu95av2_dbconn(), "DBSCHEMA")
dbmeta(hgu95av2_dbconn(), "DBSCHEMAVERSION")
library("DBI")
dbListTables(hgu95av2_dbconn()) #lists all tables on connection
## If you use dbSendQuery instead of dbGetQuery
## (NOTE: for ease of use, this is defintitely NOT reccomended)
## Then you may need to know how to list results objects
dbListResults(hgu95av2_dbconn()) #for listing results objects
## You can also list the fields by using this connection
dbListFields(hgu95av2_dbconn(), "probes")
dbListFields(hgu95av2_dbconn(), "genes")
dbschema(hgu95av2ENTREZID) # same as hgu95av2_dbschema()
## According to the schema, the probes._id column references the genes._id
## column. Note that in all tables, the "_id" column is an internal id with
## no biological meaning (provided for allowing efficient joins between
## tables).
## The information about the probe to gene mapping is in probes:
dbGetQuery(hgu95av2_dbconn(), "SELECT * FROM probes LIMIT 10")
## This mapping is in fact the ENTREZID map:
toTable(hgu95av2ENTREZID)[1:10, ] # only relevant columns are retrieved
dbInfo(hgu95av2GO) # same as hgu95av2_dbInfo()
##Advanced example:
##Sometimes you may wish to join data from across multiple databases at
##once:
## In the following example we will attach the GO database to the
## hgu95av2 database, and then grab information from separate tables
## in each database that meet a common criteria.
library(hgu95av2.db)
library("GO.db")
attachSql <- paste('ATTACH "', GO_dbfile(), '" as go;', sep = "")
dbGetQuery(hgu95av2_dbconn(), attachSql)
sql <- 'SELECT DISTINCT a.go_id AS "hgu95av2.go_id",
a._id AS "hgu95av2._id",
g.go_id AS "GO.go_id", g._id AS "GO._id",
g.term, g.ontology, g.definition
FROM go_bp_all AS a, go.go_term AS g
WHERE a.go_id = g.go_id LIMIT 10;'
data <- dbGetQuery(hgu95av2_dbconn(), sql)
data
## For illustration purposes, the internal id "_id" and the "go_id"
## from both tables is included in the output. This makes it clear
## that the "go_ids" can be used to join these tables but the internal
## ids can NOT. The internal IDs (which are always shown as _id) are
## suitable for joins within a single database, but cannot be used
## across databases.
}
\keyword{classes}
\keyword{methods}
|
