plotBranchpointWindow {branchpointer} | R Documentation

## Plots branchpointer predictions

### Description

Plots branchpointer predictions

### Usage

    plotBranchpointWindow(queryName, predictions, probabilityCutoff = 0.52,
      plotMutated = FALSE, plotStructure = TRUE, exons)

### Arguments

`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()

### Value

ggplot2 plot with branchpoint features in the specified intronic region

### 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)
    plotBranchpointWindow(querySNP$id[1], predictionsSNP,
    plotMutated = TRUE, exons = exons)

[Package branchpointer version 1.20.0 Index]