matchEnhancers: GRanges method to match enhancers with putative targets sites

Description Methods Examples

Description

GRanges method to match enhancers with putative targets sites (either TSS or TF-bound TSS)

Methods

To be used in this form:

matchEnhancers(enhGR, minD=2e4, maxD=2e5, txdb, EG2GS, TFGR=NULL)

where:

This methods relies on a previous identification of enhancer sites, as the one performed by the enhancers compEpiTools method based on H3K4me1 peaks (or alternatively H3K27ac, mediator, ..). Genomic regions which are evaluated as putative target sites of these enhancers are either transcription start sites (TSS) or TSS which are bound at least by a transcription factor (TF) whose binding sites are provided wuth TFGR.

Putative target sites of the provided enhancers are here defined based on the maximum and minimum distance from an enhancer. In addition, no additional TSS (belonging to differe genes, isoforms of the same gene do not count) have to be in between the enhancer and the reference target region.

If a set of TF bound regions is also provided, which is supposed to contain binding sites at the level of promoters, this method returns a list with 5 items:

otherwise this method returns a list with 3 items

Examples

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	require(org.Mm.eg.db)
	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)
	enh <- enhancers(H3K4me1GR, txdb)
	m.enh <- matchEnhancers(enhGR=enh, minD=2e4, maxD=2e5, 
		txdb=txdb, EG2GS=org.Mm.eg.db)

kamalfartiyal84/compEpiTools documentation built on May 29, 2019, 5:40 a.m.