regions-methods: regions-methods

In RnBeads: RnBeads

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))

RnBeads documentation built on March 3, 2021, 2 a.m.