| predictionsToSummary {branchpointer} | R Documentation |
Takes predictions of branchpoint probabilities from a reference and alternative SNP and summarises the effect(s) of the SNP.
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 = |
probabilityChange |
Minimum probability score change
required to call a branchpoint site as deleted or created by
a SNP (default = |
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)