annotation,RnBSet-method {RnBeads} | R Documentation

## annotation-methods

### Description

Genomic annotation of the methylation sites or regions covered in the supplied dataset.

### Usage

    ## S4 method for signature 'RnBSet'
    annotation(object, type = "sites",
      add.names = FALSE, include.regions = FALSE)

### Arguments

`object` | dataset as an object of type inheriting `RnBSet`.
`type` | loci or regions for which the annotation should be obtained. If the value of this parameter is `"sites"` (default), individual methylation sites are annotated. Otherwise, this must be one of the available region types, as returned by `rnb.region.types`.
`add.names` | flag specifying whether the unique site identifiers should be used as row names of the resulting data frame
`include.regions` | if `TRUE` one additional column is added to the returned annotation dat frame for each of the available region types, giving the indices of the

### Value

Annotation table in the form of a `data.frame`.

### Author(s)

Pavlo Lutsik

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    ## show present sites
    head(annotation(rnb.set.example, add.names=TRUE))
    ## show promoters
    ann.prom<-annotation(rnb.set.example, type="promoters", add.names=TRUE)
    head(ann.prom)

[Package RnBeads version 2.2.0 Index]