EventPointer_Bootstraps: EventPointer_Bootstraps

In jpromeror/EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data

EventPointer_Bootstraps

Description

Statistical analysis of alternative splicing events with bootstrap technique.

Usage

EventPointer_Bootstraps(
  PSI,
  Design,
  Contrast,
  cores = 1,
  ram = 0.1,
  nBootstraps = 10000,
  UsePseudoAligBootstrap = TRUE,
  Threshold = 0
)

Arguments

PSI	Array or matrix that contains the values of PSI calculated in the function GetPSIFromTranRef. If bootstrap option was selected in GetPSIFromTranRef, input must be an array. If not, input must be a matrix
Design	Design matrix
Contrast	Contrast matrix
cores	The number of cores desired to use.
ram	How many ram memory is used,in Gb.
nBootstraps	How many layers, Bootstraps or samplings are going to be used. Caution, high numbers increase computational time.
UsePseudoAligBootstrap	TRUE (default) if bootstrap data from pseudoaligment want to be used or FALSe if not.
Threshold	it assigns a threshold to compute the pvalues. default = 0.

Value

A list containing the summary of the Bootstrap analysis: DeltaPSI, Pvalues, FDR. This info can be obtained in a simple table with the function ResulTable.

Examples

       data(PSIss)
       PSI <- PSIss$PSI
       
       Dmatrix <- cbind(1,rep(c(0,1),each=2))
       Cmatrix <- matrix(c(0,1),nrow=2)
       
       Fit <- EventPointer_Bootstraps(PSI = PSI,
                                      Design = Dmatrix,
                                      Contrast = Cmatrix,
                                      cores = 1,
                                      ram = 1,
                                      nBootstraps = 10,
                                      UsePseudoAligBootstrap = TRUE)

jpromeror/EventPointer documentation built on May 17, 2023, 10:29 p.m.