% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/CDFfromGTF_Multipath.R
 \name{CDFfromGTF_Multipath}
 \alias{CDFfromGTF_Multipath}

 \title{CDF file creation for EventPointer (MultiPath)}

 \usage{

 CDFfromGTF_Multipath(
   input = "Ensembl",
   inputFile = NULL,
   PSR,
   Junc,
   PathCDF,
   microarray = NULL,
   paths = 2
 )

 }
 \arguments{

 \item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,
 UCSC or GTF.}

 
 \item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.}
 
 \item{PSR}{Path to the Exon probes txt file}
 
 \item{Junc}{Path to the Junction probes txt file}
 
 \item{PathCDF}{Directory where the output will be saved}
 

 \item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0,
 ClariomD, RTA or MTA}

 
 \item{paths}{Maximum number of paths of the events to find.}
 }
 \value{

 The function displays a progress bar to show the user the progress of the function.

 However, there is no value returned in R as the function creates three files that are used

 later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all
 the information of all the alternative splcing events found. 2) .flat file : Used to build
 the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing
 pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is

 recommended to have at least 1.5 GB of free space.
 }
 \description{

 Generates the CDF file to be used under the aroma.affymetrix framework.

 }
 \examples{

  \dontrun{

    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()

    microarray<-'HTA-2_0'

 
   # Run the function
 

    CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,
                         PathCDF=Directory,microarray=microarray,paths=3)

  }

 
 }