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

In branchpointer: Prediction of intronic splicing branchpoints

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

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