EventPointer: EventPointer

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

EventPointer

Description

Statistical analysis of alternative splcing events

Usage

EventPointer(
  Design,
  Contrast,
  ExFit,
  Eventstxt,
  Filter = TRUE,
  Qn = 0.25,
  Statistic = "LogFC",
  PSI = FALSE
)

Arguments

Design	The design matrix for the experiment.
Contrast	The contrast matrix for the experiment.
ExFit	aroma.affymetrix pre-processed variable after using extractDataFrame(affy, addNames=TRUE)
Eventstxt	Path to the EventsFound.txt file generated by CDFfromGTF function.
Filter	Boolean variable to indicate if an expression filter is applied
Qn	Quantile used to filter the events (Bounded between 0-1, Q1 would be 0.25).
Statistic	Statistical test to identify differential splicing events, must be one of : LogFC, Dif_LogFC or DRS.
PSI	Boolean variable to indicate if Delta PSI should be calculated for every splicing event.

Value

Data.frame ordered by the splicing p.value . The object contains the different information for each splicing event such as Gene name, event type, genomic position, p.value, z.value and delta PSI.

Examples

   data(ArraysData)

   Dmatrix<-matrix(c(1,1,1,1,0,0,1,1),nrow=4,ncol=2,byrow=FALSE)
   Cmatrix<-t(t(c(0,1)))
   EventsFound<-paste(system.file('extdata',package='EventPointer'),'/EventsFound.txt',sep='')

   Events<-EventPointer(Design=Dmatrix,
                        Contrast=Cmatrix,
                        ExFit=ArraysData,
                        Eventstxt=EventsFound,
                        Filter=TRUE,
                        Qn=0.25,
                        Statistic='LogFC',
                        PSI=TRUE)

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