EventPointer_IGV: EventPointer IGV Visualization

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

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

## Not run: 
   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')
                 

## End(Not run)

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