calculatePSIValues: PSI value calculation

In c-mertes/FraseR: Find RAre Splicing Events in RNA-Seq Data

PSI value calculation

Description

This function calculates the PSI values for each junction and splice site based on the FraserDataSet object

Usage

calculatePSIValues(
  fds,
  types = psiTypes,
  overwriteCts = FALSE,
  BPPARAM = bpparam()
)

Arguments

fds	A FraserDataSet object
types	A vector with the psi types which should be calculated. Default is all of jaccard, psi5, psi3 and theta.
overwriteCts	FALSE or TRUE (the default) the total counts (aka N) will be recalculated based on the existing junction counts (aka K)
BPPARAM	the BiocParallel parameters for the parallelization

Value

FraserDataSet

Examples

  fds <- createTestFraserDataSet()
  fds <- calculatePSIValues(fds, types="jaccard")
  
  ### usually one would run this function for all psi types by using:
  # fds <- calculatePSIValues(fds)

c-mertes/FraseR documentation built on April 21, 2024, 1:22 a.m.