getMeth: getMeth to extract DNA methylation slot from a MEE.data class...

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

getMeth is a function to easily extract DNA methylation data out of a MEE.data object. By specifying probe or ID for samples, a matrix of DNA methylation values for defined probes and samples will be extracted out of MEE.data object.

Usage

getMeth(object, probe, ID)

## S4 method for signature 'MEE.data'
getMeth(object, probe, ID)

Arguments

object	MEE.data object
probe	A vector of probes' name. When specified, DNA methylation only for these probes will be output.
ID	A vector of sample ID. When specified, DNA methylation only for these samples will be output.

Value

A matrix of DNA methylation values.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

meth <- matrix(data=c(1:20),ncol=5,dimnames=list(paste0("probe",1:4),paste0("sample",1:5)))
mee <- fetch.mee(meth=meth)
Meth <- getMeth(mee,probe = "probe1")
Meth <- getMeth(mee, ID = c("sample1","sample2"))

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.