predictionsToSummary: Convert SNP branchpoint predictions across the branchpoint...
In branchpointer: Prediction of intronic splicing branchpoints

Description Usage Arguments Value Author(s) Examples

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

1 2	predictionsToSummary(query, predictions, probabilityCutoff = 0.52, probabilityChange = 0.15)

`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`)

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

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)

summarySNP <- predictionsToSummary(querySNP,predictionsSNP)