annotation-methods: annotation-methods

In RnBeads: RnBeads

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)

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