CDFfromGTF_Multipath: CDF file creation for EventPointer (MultiPath)

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

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)

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