man/CDFfromGTF_Multipath.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/CDFfromGTF_Multipath.R
 \name{CDFfromGTF_Multipath}
 \alias{CDFfromGTF_Multipath}
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 \title{CDF file creation for EventPointer (MultiPath)}
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 \usage{
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 CDFfromGTF_Multipath(
   input = "Ensembl",
   inputFile = NULL,
   PSR,
   Junc,
   PathCDF,
   microarray = NULL,
   paths = 2
 )
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 }
 \arguments{
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 \item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,
 UCSC or GTF.}
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 \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}
 
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 \item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0,
 ClariomD, RTA or MTA}
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 \item{paths}{Maximum number of paths of the events to find.}
 }
 \value{
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 The function displays a progress bar to show the user the progress of the function.
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 However, there is no value returned in R as the function creates three files that are used
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 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
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 recommended to have at least 1.5 GB of free space.
 }
 \description{
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 Generates the CDF file to be used under the aroma.affymetrix framework.
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 }
 \examples{
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  \dontrun{
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    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()
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    microarray<-'HTA-2_0'
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   # Run the function
 
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    CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,
                         PathCDF=Directory,microarray=microarray,paths=3)
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  }
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 }