predictionsToSummary {branchpointer} | R Documentation

## Convert SNP branchpoint predictions across the branchpoint window to an intronic summary

### 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)

[Package branchpointer version 1.16.0 Index]