EventPointer_IGV {EventPointer} | R Documentation

## EventPointer IGV Visualization

### Description

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

### Usage

    EventPointer_IGV(Events, input, inputFile = NULL, PSR, Junc, PathGTF,
      EventsFile, microarray = NULL)

### Arguments

`Events` | Data.frame generated by EventPointer with the events to be included in the GTF file.
`input` | Reference transcriprome. Must be one of: 'Ensembl', 'UCSC' , 'AffyGTF' or 'CustomGTF'.
`inputFile` | If input is 'AffyGTF' or 'CustomGTF', inputFile should point to the GTF file to be used.
`PSR` | Path to the Exon probes txt file.
`Junc` | Path to the Junction probes txt file.
`PathGTF` | Directory where to write the GTF files.
`EventsFile` | Path to EventsFound.txt file generated with CDFfromGTF function.
`microarray` | Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA

### Value

The function displays a progress bar to show the user the progress of the function. Once the progress bar reaches 100 in PathGTF. The created files are: 1) paths.gtf : GTF file representing the alternative splicing events and 2) probes.gtf : GTF file representing the probes that measure each event and each path.

### Examples

       PathFiles<-system.file('extdata',package='EventPointer')
       DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='')
       PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')
       JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='')
       Directory<-tempdir()

       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_IGV(Events=Events[1,,drop=FALSE],
                      input='AffyGTF',
                      inputFile=DONSON_GTF,
                      PSR=PSRProbes,
                      Junc=JunctionProbes,
                      PathGTF=Directory,
                     EventsFile= EventsFound,
                     microarray='HTA-2_0')

[Package EventPointer version 2.5.5 Index]