compEpiTools (version 1.6.3)

GRangesInPromoters-methods: Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters

Description

Subset a GRanges returning only those ranges which are overlapping (at least 1bp) with promoters

Methods

This method subsets a GRanges returning only those ranges which are overlapping, or not, with promoters defined based on a TxDb, upstream and downstream distance from TSS. To be used in this form: GRangesInPromoters(Object, txdb, upstream=2000, downstream=1000, invert=FALSE) where:

• Object: GRanges
• txdb: TxDb
• upstream: numeric
• downstream: numeric
• invert: logical; see below

Promoters are defined based on upstream and downstream distances from Transcription Start Sites (TSS). If invert if FALSE, the subset of Object overlapping with promoter regions is returned, if any, otherwise NULL is returned. If invert if TRUE, the subset of Object which is not overlapping with promoter regions is returned, if any, otherwise NULL is returned.

Examples

require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb<- TxDb.Mmusculus.UCSC.mm9.knownGene
TSSpos <- TSS(txdb)
gr <- TSSpos[1:5]
start(gr) <- start(gr) - 1000
end(gr) <- end(gr) - 600
GRangesInPromoters(Object=gr, txdb=txdb, upstream=2000, downstream=1000)