plotBranchpointWindow: Plots branchpointer predictions

In branchpointer: Prediction of intronic splicing branchpoints

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)

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