calculatePSIValues: PSI value calculation

View source: R/calculatePSIValue.R

calculatePSIValuesR Documentation

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 June 15, 2024, 3:29 a.m.