estimateCMR.methylation {methyAnalysis} | R Documentation |
Estimate the averaged methylation levels within a chromosome region defined as a GRanges object or transcript promoter
estimateCMR.methylation(cmr, methyGenoSet, estimateFun = mean, probeAnnotation = NULL, selectGeneElement = c("exon1", "promoter"), mc.cores = min(12, detectCores()))
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 |
A numeric matrix (row: cmr, column: samples)
Pan DU