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 1.19.0 Index]