R: AnnotationDb objects and their progeny, methods etc.

AnnotationDb-objects {AnnotationDbi}

R Documentation

AnnotationDb objects and their progeny, methods etc.

Description

AnnotationDb is the virtual base class for all annotation packages. It contain a database connection and is meant to be the parent for a set of classes in the Bioconductor annotation packages. These classes will provide a means of dispatch for a widely available set of select methods and thus allow the easy extraction of data from the annotation packages.

select, cols and keys are used together to extract data from an AnnotationDb object (or any object derived from the parent class). Examples of classes derived from the AnnotationDb object include (but are not limited to): ChipDb, OrgDb and GODb.

cols shows which kinds of data can be returned for the AnnotationDb object.

keytypes allows the user to discover which keytypes can be passed in to select or keys and the keytype argument.

keys returns keys for the database contained in the AnnotationDb object . This method is already documented in the keys manual page but is mentioned again here because it's usage with select is so intimate. By default it will return the primary keys for the database, but if used with the keytype argument, it will return the keys from that keytype.

select will retrieve the data as a data.frame based on parameters for selected keys and cols and keytype arguments.

saveDb will take an AnnotationDb object and save the database to the file specified by the path passed in to the file argument.

loadDb takes a .sqlite database file as an argument and uses data in the metadata table of that file to return an AnnotationDb style object of the appropriate type.

Usage

  cols(x)
  keytypes(x)
  select(x, keys, cols, keytype, ...)

  saveDb(x, file)
  loadDb(file, dbType, dbPackage, ...)

Arguments

`x`	the `AnnotationDb` object. But in practice this will mean an object derived from an `AnnotationDb` object such as a `OrgDb` or `ChipDb` object.
`keys`	the keys to select records for from the database. All possible keys are returned by using the `keys` method.
`cols`	the cols or kinds of things that can be retrieved from the database. As with `keys`, all possible cols are returned by using the `cols` method.
`keytype`	the keytype that matches the keys used. For the `select` methods, this is used to indicate the kind of ID being used with the keys argument. For the `keys` method this is used to indicate which kind of keys are desired from `keys`
`file`	an `sqlite` file path. A string the represents the full name you want for your sqlite database and also where to put it.
`dbType`	dbType - not required
`dbPackage`	dbPackage - not required
`...`	other arguments

Value

keys,cols and keytypes each return a character vector or possible values. select returns a data.frame.

Author(s)

Marc Carlson

Examples

require(hgu95av2.db)
## display the cols
cols(hgu95av2.db)
## get the 1st 6 possible keys
keys <- head( keys(hgu95av2.db) )
keys
## lookup gene symbol and unigene ID for the 1st 6 keys
select(hgu95av2.db, keys=keys, cols = c("SYMBOL","UNIGENE"))

## get keys based on unigene
keyunis <- head( keys(hgu95av2.db, keytype="UNIGENE") )
keyunis
## list supported key types
keytypes(hgu95av2.db)
## lookup gene symbol and unigene ID based on unigene IDs by setting
## the keytype to "UNIGENE" and passing in unigene keys:
select(hgu95av2.db, keys=keyunis, cols = c("SYMBOL","UNIGENE"),
       keytype="UNIGENE")

[Package AnnotationDbi version 1.16.0 Index]