predictBranchpoints {branchpointer} | R Documentation |
predicts branchpoint probability scores for each query site.
predictBranchpoints(query, uniqueId = "test", queryType, workingDirectory = ".", genome = NA, bedtoolsLocation = NA, BSgenome = NULL, useParallel = FALSE, cores = 1, rmChr = FALSE)
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 = |
rmChr |
remove "chr" before chromosome names before writing bed file. Required if genome sequence names do not contain "chr" |
GenomicRanges object with branchpoint probaility scores for each site in query
Beth Signal
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)