makeBranchpointWindowForExons {branchpointer} | R Documentation

## Make branchpoint window regions

### 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)

[Package branchpointer version 1.12.0 Index]