EventPointer_IGV: EventPointer IGV Visualization

Description Usage Arguments Value Examples

View source: R/EventPointer_IGV.R

Description

Generates of files to be loaded in IGV for visualization and interpretation of events

Usage

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EventPointer_IGV(Events, input, inputFile = NULL, PSR, Junc, PathGTF,
  EventsFile, microarray = NULL)

Arguments

Events

Data.frame generated by EventPointer with the events to be included in the GTF file.

input

Reference transcriprome. 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.

PathGTF

Directory where to write the GTF files.

EventsFile

Path to EventsFound.txt file generated with CDFfromGTF function.

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. Once the progress bar reaches 100 in PathGTF. The created files are: 1) paths.gtf : GTF file representing the alternative splicing events and 2) probes.gtf : GTF file representing the probes that measure each event and each path.

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()

   data(ArraysData)

   Dmatrix<-matrix(c(1,1,1,1,0,0,1,1),nrow=4,ncol=2,byrow=FALSE)
   Cmatrix<-t(t(c(0,1)))
   EventsFound<-paste(system.file('extdata',package='EventPointer'),'/EventsFound.txt',sep='')

   Events<-EventPointer(Design=Dmatrix,
                      Contrast=Cmatrix,
                      ExFit=ArraysData,
                      Eventstxt=EventsFound,
                      Filter=TRUE,
                      Qn=0.25,
                      Statistic='LogFC',
                      PSI=TRUE)

 EventPointer_IGV(Events=Events[1,,drop=FALSE],
                  input='AffyGTF',
                  inputFile=DONSON_GTF,
                  PSR=PSRProbes,
                  Junc=JunctionProbes,
                  PathGTF=Directory,
                 EventsFile= EventsFound,
                 microarray='HTA-2_0')

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