EventPointer_IGV {EventPointer} | R Documentation |
Generates of files to be loaded in IGV for visualization and interpretation of events
EventPointer_IGV( Events, input, inputFile = NULL, PSR, Junc, PathGTF, EventsFile, microarray = NULL )
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 |
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.
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')