EventPointer: EventPointer

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

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)

EventPointer documentation built on Nov. 8, 2020, 7:12 p.m.