getRoadMapEnhancerProbes: getRoadMapEnhancerProbes

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

getRoadMapEnhancerProbes

Description

getRoadMapEnhancerProbes

Usage

getRoadMapEnhancerProbes(
  met.platform = "EPIC",
  genome = "hg38",
  functional.regions = c("EnhA1", "EnhA2"),
  listOfEpigenomes = NULL,
  ProbeAnnotation
)

Arguments

met.platform	character string indicating the methylation platform, can be either 'EPIC' or 'HM450'
genome	character string indicating the genome build version, can be either 'hg19' or 'hg38'
functional.regions	character vector indicating the MNEMONIC chromatin states that will be retrieved from the Roadmap epigenomics. Default values are the active enhancers:'EnhA1', 'EnhA2'.
listOfEpigenomes	character vector indicting which epigenome(s) to use for finding enhancers.
ProbeAnnotation	GRange object of probe annotation.

Details

get the CpG probes that locate at the enhancer regions identified by the Roadmap epigenomics project

Value

a dataframe with enhancer probes and their chromosome coordinates

Examples

met.platform = 'EPIC'
genome = 'hg38'
listOfEpigenomes = c('E034', 'E045', 'E047')
functional.regions = c('EnhA1', 'EnhA2', 'EnhG1', 'EnhG2')
df.enhancer.probes <-  getEnhancerProbes(met.platform = met.platform,
                                        genome = genome,
                                        functional.regions = functional.regions,
                                        listOfEpigenomes = listOfEpigenomes)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.