estimateCMR.methylation {methyAnalysis} | R Documentation

## Estimate the averaged methylation levels within a chromosome region or transcript promoter

### Description

Estimate the averaged methylation levels within a chromosome region defined as a GRanges object or transcript promoter

### Usage

    estimateCMR.methylation(cmr, methyGenoSet, estimateFun = mean, probeAnnotation = NULL, selectGeneElement = c("exon1", "promoter"), mc.cores = min(12, detectCores()))

### Arguments

`cmr` | A GRanges object or transcript ID
`methyGenoSet` | A MethyGenoSet object keeps the DNA methylation data
`estimateFun` | The function used to estimate the methylation levels within the chromosome region
`probeAnnotation` | Pre-calculated probe annotation (a GRanges object)
`selectGeneElement` | Gene elements used to calculate the transcript promoter methylation levels if cmr GRanges object is not provided.
`mc.cores` | Number of cores used to calculate in parallel

### Value

A numeric matrix (row: cmr, column: samples)

### Author(s)

Pan DU

[Package methyAnalysis version 1.28.0 Index]