CDFfromGTF: CDF file creation for EventPointer

Description Usage Arguments Value Examples

View source: R/CDFfromGTF.R

Description

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

Usage

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CDFfromGTF(input = "Ensembl", inputFile = NULL, PSR, Junc, PathCDF,
  microarray = NULL)

Arguments

input

Reference transcriptome used to build the CDF file. 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

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

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

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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()
   microarray<-'HTA-2_0'

  # Run the function

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

EventPointer documentation built on Nov. 8, 2020, 7:12 p.m.