rnb.get.annotation {RnBeads} | R Documentation

## rnb.get.annotation

### Description

Extracts the requested annotation for the given genome.

### Usage

    rnb.get.annotation(type = "CpG", assembly = "hg19")

### Arguments

`type` | Name of annotation.
`assembly` | Genome assembly of interest. See `rnb.get.assemblies` for the list of supported genomes.

### Details

When the returned value is of type `GRangesList`, it defines the genomic positions of the requested sites, probes or regions. Identifiers, if present, can be obtained using the `names` method. Strand information is also included when applicable. Any additional annotation is stored as metadata in the respective `GRanges` objects.

### Value

Probe, site or region annotation table. If the specified type refers to control probes, the returned value is a `data.frame` listing all respective control probes. Otherwise, this function returns an object of type `GRangesList` - a list of consistent `GRanges` objects, one per chromosome.

### Author(s)

Fabian Mueller

### See Also

`rnb.set.annotation` for adding annotation; `rnb.region.types` for all loaded region types in a genome assembly

### Examples

    rnb.get.annotation("promoters")

[Package RnBeads version 2.0.1 Index]