predictionsToSummary: Convert SNP branchpoint predictions across the branchpoint...

In betsig/branchpointer: Prediction of intronic splicing branchpoints

Description

Takes predictions of branchpoint probabilities from a reference and alternative SNP and summarises the effect(s) of the SNP.

Usage

predictionsToSummary(query, predictions, probabilityCutoff = 0.52,
  probabilityChange = 0.15)

Arguments

query	query GRanges containing all SNP ids to be summarised
predictions	site-wide branchpoint proability predictions produced from predictBranchpoints()
probabilityCutoff	Value to be used as the cutoff for discriminating branchpoint sites from non-branchpoint sites (default = 0.52)
probabilityChange	Minimum probability score change required to call a branchpoint site as deleted or created by a SNP (default = 0.15)

Value

GRanges with summarised branchpoint changes occuring within the intron due to a SNP.

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)

summarySNP <- predictionsToSummary(querySNP,predictionsSNP)

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