predictBranchpoints: Predict branchpoint probability scores

In betsig/branchpointer: Prediction of intronic splicing branchpoints

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)

betsig/branchpointer documentation built on Sept. 27, 2021, 10:31 p.m.