EventPointer_RNASeq_IGV {EventPointer} | R Documentation

## EventPointer RNASeq IGV Visualization

### 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)

[Package EventPointer version 3.2.0 Index]