predictBranchpoints {branchpointer} | R Documentation

## Predict branchpoint probability scores

### Description

predicts branchpoint probability scores for each query site.

### Usage

    predictBranchpoints(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 object with branchpoint probaility scores for each site in query

### Author(s)

Beth Signal

### Examples

    smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf",
    package = "branchpointer")
    exons <- gtfToExons(smallExons)
    g <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

    querySNPFile <- system.file("extdata","SNP_example.txt", package = "branchpointer")
    querySNP <- readQueryFile(querySNPFile,queryType = "SNP",exons = exons, filter = FALSE)
    predictionsSNP <- predictBranchpoints(querySNP,queryType = "SNP",BSgenome = g)

[Package branchpointer version 1.6.0 Index]