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("db", "env"))

### 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, and then the default value of `type` takes over.

### Details

`getAnnMap` uses the search path (see `search`) to find an appropriate annotation data package; when called with `chip="hgu95av2"`, the function will use the first hgu95av2 package on the search path whether it be db or environment-based. If `load=TRUE` and no suitable package is found on the search path, then the function will attempt to load an appropriate package. The `type` argument is used to determine which type of package (db or env) is loaded first.

### Value

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

### Author(s)

Seth Falcon

### Examples

    map <- getAnnMap("ENTREZID", "hgu95av2", load=TRUE, type=c("env", "db"))
    class(map)

[Package annotate version 1.62.0 Index]