makeBranchpointWindowForExons: Make branchpoint window regions

In betsig/branchpointer: Prediction of intronic splicing branchpoints

Description

Generate branchpoint window regions corresponding to annotated exon(s) within a queried gene, transcript or exon id

Usage

makeBranchpointWindowForExons(id, idType, exons, forceClosestExon = FALSE)

Arguments

id	identifier(s) for the query gene/transcript/exon id
idType	type of id to match in the exon annotation file ("gene_id", "transcript_id", or "exon_id")
exons	GRanges containing exon co-ordinates.
forceClosestExon	Force branchpointer to find the closest exon and not the exon annotated as 5' to the query

Value

Granges with formatted query

Author(s)

Beth Signal

Examples

smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf",package = "branchpointer")
exons <- gtfToExons(smallExons)
windowquery <- makeBranchpointWindowForExons("ENSG00000139618.14", "gene_id", exons)
windowquery <- makeBranchpointWindowForExons("ENST00000357654.7", "transcript_id", exons)
windowquery <- makeBranchpointWindowForExons("ENSE00003518965.1", "exon_id", exons)

betsig/branchpointer documentation built on Sept. 27, 2021, 10:31 p.m.