plotBranchpointWindow: Plots branchpointer predictions

Description Usage Arguments Value Author(s) Examples

View source: R/plotBranchpointWindow.R

Description

Plots branchpointer predictions

Usage

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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

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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)

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