compEpiTools (version 1.6.3)

GRannotateSimple-methods: a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic

Description

Given a GRanges and a TxDB object, the GRanges are divided according to their overlap to promoters (defined based on upstream and downstream bp from transcription start sites, TSS) and genebody (intragenic), while the remaining GRanges are assigned to intergenic

Methods

To be used in this form: GRannotateSimple(gr, txdb, upstream=2000, downstream=1000) where:

• gr: a GRanges
• txdb: an object of class TxDB
• upstream: numeric; the number of bp upstream the TSS
• downstream: numeric; the number of bp downstream the TSS

Examples

	require(TxDb.Mmusculus.UCSC.mm9.knownGene)
	txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
	gr <- GRanges(Rle(c('chr1','chr1')), 
		ranges=IRanges(start=c(100,200), end=c(150,250)))
	GRannotateSimple(gr, txdb)