meth-methods: meth-methods

Description Usage Arguments Value See Also Examples

Description

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

Usage

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## 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

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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 May 9, 2018, 6:01 p.m.