meth-methods: meth-methods

In RnBeads: RnBeads

Description

Extracts DNA methylation information (beta values) for a specified set of genomic features.

Usage

## S4 method for signature 'RnBSet'
meth(object, type = "sites", row.names = FALSE, i = NULL, j = NULL)

Arguments

object	dataset of interest.
type	character singleton. If this is set to "sites" (default), DNA methylation information for each available site is returned. Otherwise, this should be one of region types for for which summarized DNA methylation information is computed in the given dataset.
row.names	flag indicating if row names are to be generated in the result.
i	indices of sites/regions to be retrieved. By default (NULL), all will be retrieved.
j	indices of samples to be retrieved. By default (NULL), all will be retrieved.

Value

matrix with methylation beta values.

See Also

mval for calculating M values

Examples

library(RnBeads.hg19)
data(small.example.object)
## per-site beta-value matrix
mm<-meth(rnb.set.example, row.names=TRUE)
head(mm)
## beta-values for each covered gene
gmm<-meth(rnb.set.example, type="gene", row.names=TRUE)
head(gmm)

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