EventPointer_RNASeq_IGV: EventPointer RNASeq IGV Visualization

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

Description

Generates of files to be loaded in IGV for visualization and interpretation of events

Usage

EventPointer_RNASeq_IGV(Events, SG_RNASeq, EventsTxt, PathGTF)

Arguments

Events	Data.frame generated by EventPointer_RNASeq with the events to be included in the GTF file.
SG_RNASeq	Output from PrepareBam_EP function. Contains splicing graphs components.
EventsTxt	Path to EventsFound.txt file generated with EventDetection function
PathGTF	Directory where to write the GTF files.

Value

The function displays a progress bar to show the user the progress of the function. Once the progress bar reaches 100 file is written to the specified directory in PathGTF. The created file: 1) paths_RNASeq.gtf : GTF file representing the alternative splicing events.

Examples

  data(AllEvents_RNASeq)
  data(SG_RNASeq)

   # Run EventPointer

   Dmatrix<-matrix(c(1,1,1,1,1,1,1,1,0,0,0,0,1,1,1,1),ncol=2,byrow=FALSE)
   Cmatrix<-t(t(c(0,1)))
   Events <- EventPointer_RNASeq(AllEvents_RNASeq,Dmatrix,Cmatrix,Statistic='LogFC',PSI=TRUE)

   # IGV Visualization

   EventsTxt<-paste(system.file('extdata',package='EventPointer'),'/EventsFound_RNASeq.txt',sep='')
   PathGTF<-tempdir()
   EventPointer_RNASeq_IGV(Events,SG_RNASeq,EventsTxt,PathGTF)

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