getBranchpointSequence {branchpointer} | R Documentation

## Get branchpoint sequence features Gets intronic sequence covering the branchpoint window and extracts predictive features

### Description

Get branchpoint sequence features Gets intronic sequence covering the branchpoint window and extracts predictive features

### Usage

    getBranchpointSequence(query, uniqueId = "test", queryType,
      workingDirectory = ".", genome = NA, bedtoolsLocation = NA,
      BSgenome = NULL, useParallel = FALSE, cores = 1, rmChr = FALSE)

### Arguments

`query` | branchpointer query GenomicRanges
`uniqueId` | unique string identifier for intermediate .bed and .fa files.
`queryType` | type of branchpointer query. "SNP" or "region".
`workingDirectory` | directory where intermediate .bed and .fa are located
`genome` | .fa genome file location
`bedtoolsLocation` | bedtools binary location (which bedtools)
`BSgenome` | BSgenome object
`useParallel` | use parallelisation to speed up code?
`cores` | number of cores to use in parallelisation (default = `1`)
`rmChr` | remove "chr" before chromosome names before writing bed file. Required if genome sequence names do not contain "chr"

### Value

GenomicRanges with all features required to predict branchpoint probability scores

### Author(s)

Beth Signal

[Package branchpointer version 1.12.0 Index]