regions,RnBSet-method {RnBeads} | R Documentation

## regions-methods

### Description

Methylation regions, information for which is present in the `RnBSet` object.

### Usage

    ## S4 method for signature 'RnBSet'
    regions(object, type = NULL)

### Arguments

`object` | Dataset of interest.
`type` | Region type(s) of interest as a `character` vector. If this is set to `NULL`, all region types summarized in the object are returned.

### Value

Methylation site and region assignment. If `type` is singleton, a `matrix` is returned. The first column corresponds to the methylation context index. The second column is the index of the chromosome in the genome, and the third is the index of the region in the `GRanges` object of the region type annotation. When `length(type)>1`, a list of such matrices is returned for each element of `type`. If `type` is `NULL`, matrices for all summarized region types are returned.

### Note

Methylation context index is an integer number denoting the sequence context of the cytosine of interest. Index `1` corresponds to `CpG`, the only supported index in bisulfite sequencing datasets.

### Author(s)

Pavlo Lutsik

### See Also

`summarized.regions` for all summarized region types in a dataset; `rnb.get.chromosomes` listing all supported chromosomes for a given genome assembly

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    head(regions(rnb.set.example))

[Package RnBeads version 2.0.1 Index]