getAnnMap {annotate}R Documentation

Get annotation map

Description

This function retrieves a map object from an annotation data package. It is intended to serve as a common interface for obtaining map objects from both SQLite-based and environment-based annotation data packages.

Usage

getAnnMap(map, chip, load = TRUE, type = c("env", "db"))

Arguments

map a string specifying the name of the map to retrieve. For example, "ENTREZID" or "GO"
chip a string describing the chip or genome
load a logical value. When TRUE, getAnnMap will try to load the annotation data package if it is not already attached.
type a character vector of one or more annotation data package types. The currently supported types are "db" and "env". If load is TRUE, you can specify both "db" and "env" and the order will determine which type is tried first. This provides a fall-back mechanism when the preferred annotation data package type is not available. If type is missing, then the first matching annotation package found in the search path will be used.

Details

getAnnMap expects the annotation data package to be loaded and attached. If load is TRUE, the package will be attached.

Value

If type is "db", an S4 object representing the requested map. If type is "env", an R environment object representing the requested map.

Warning

SQLite-based annotation data packages are planned for the BioC 2.1 release. Use of type="db" may not work as desired in this release. In the next release, the order of "env" and "db" will be reversed to give preference to the SQLite-based packages.

Author(s)

Seth Falcon

Examples

map <- getAnnMap("ENTREZID", "hgu95av2")
class(map)

[Package annotate version 1.14.1 Index]