enhancers: A GRanges method to define enhancers based on H3K4me1 peaks
In kamalfartiyal84/compEpiTools: Tools for computational epigenomics

A GRanges method to define enhancers based on H3K4me1 peaks and genome annotation

To be used in this form:

enhancers(gr, txdb, upstream= 2000, downstream= 1000, CGIgr=NULL)

where:

gr: a GRanges, typically of H3K4me1 peaks
txdb: an object of class TxDB
upstream: numeric; the number of bp upstream the TSS
downstream: numeric; the number of bp downstream the TSS
CGIgr: GRanges; optional GRanges of CpG Islands (CGI)

Enhancers are defined as distal H3K4me1 peaks not overlapping with CGI, to avoid unannotated transcriptional units. Distal peaks are those peaks not overlapping with promoters. Alternative marks or proteins, such as H3K27ac or mediator, could be used here in place of H3K4me1. For example, H3K27ac would specifically allow to identify active enhancers.

	require(TxDb.Mmusculus.UCSC.mm9.knownGene)
	txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
	# loading H3K4me1 peaks as a GRanges object
  	# built based on the BED file from the GEO GSM1234488 sample
  	# limited to chr19:3200000-4000000
  	H3K4me1GR <- system.file("extdata", "H3K4me1GR.Rda", package="compEpiTools")
  	load(H3K4me1GR)
	enhancers(H3K4me1GR, txdb)