estimateCMR.methylation: Estimate the averaged methylation levels within a chromosome...

In methyAnalysis: DNA methylation data analysis and visualization

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

methyAnalysis documentation built on Nov. 8, 2020, 8:09 p.m.