plotBranchpointWindow {branchpointer} | R Documentation |
Plots branchpointer predictions
plotBranchpointWindow(queryName, predictions, probabilityCutoff = 0.52, plotMutated = FALSE, plotStructure = TRUE, exons)
queryName |
query id used to identify the SNP or region |
predictions |
Granges object generated by predictBranchpoints() |
probabilityCutoff |
probability score cutoff value for displaying U2 binding energy |
plotMutated |
plot alternative sequence predicitons alongside reference sequence predictions |
plotStructure |
plot structures for gene and 3' exon containing and skipping isoforms |
exons |
Granges containing exon co-ordinates. Should be produced by gtfToExons() |
ggplot2 plot with branchpoint features in the specified intronic region
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) plotBranchpointWindow(querySNP$id[1], predictionsSNP, plotMutated = TRUE, exons = exons)