getBranchpointSequence: Get branchpoint sequence features Gets intronic sequence...

Description Usage Arguments Value Author(s)

View source: R/predictBranchpoints.R

Description

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

Usage

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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


branchpointer documentation built on Nov. 8, 2020, 6:16 p.m.