RnBeads (version 1.4.0)

annotation,RnBSet-method: annotation-methods

Description

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

Usage

"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.

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)