enhancers: A GRanges method to define enhancers based on H3K4me1 peaks

Description Methods Examples

Description

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

Methods

To be used in this form:

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

where:

Examples

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	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)

kamalfartiyal84/compEpiTools documentation built on May 22, 2018, 7:50 p.m.