CDFfromGTF_Multipath {EventPointer} | R Documentation

## CDF file creation for EventPointer (MultiPath)

### Description

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

### Usage

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

### Arguments

`input` | Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.
`inputFile` | If input is GTF, 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
`PathCDF` | Directory where the output will be saved
`microarray` | Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA
`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.

### 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()
       microarray<-'HTA-2_0'

      # Run the function

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

[Package EventPointer version 3.0.0 Index]