GRannotateSimple: a GRanges method to split a GRanges in three GRanges:...

Description Methods Examples

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:

Examples

1
2
3
4
5
	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)

compEpiTools documentation built on Nov. 8, 2020, 5:32 p.m.