RnBeads (version 1.4.0)

mval,RnBSet-method: mval-methods

Description

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

Usage

"mval"(object, type = "sites", row.names = FALSE, epsilon = 0)

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 of row names are to be generated in the result.

epsilon

Threshold of beta values to use when adjusting for potential M values close to +infinity or -infinity. See rnb.beta2mval for more details.

Value

matrix with methylation M values.

See Also

meth for extracting methylation beta values

Examples

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