EventPointer_RNASeq_IGV {EventPointer} | R Documentation |
Generates of files to be loaded in IGV for visualization and interpretation of events
EventPointer_RNASeq_IGV(Events, SG_RNASeq, EventsTxt, PathGTF)
Events |
Data.frame generated by EventPointer_RNASeq with the events to be included in the GTF file. |
SG_RNASeq |
Output from PrepareBam_EP function. Contains splicing graphs components. |
EventsTxt |
Path to EventsFound.txt file generated with EventDetection function |
PathGTF |
Directory where to write the GTF files. |
The function displays a progress bar to show the user the progress of the function. Once the progress bar reaches 100 file is written to the specified directory in PathGTF. The created file: 1) paths_RNASeq.gtf : GTF file representing the alternative splicing events.
data(AllEvents_RNASeq) data(SG_RNASeq) # Run EventPointer Dmatrix<-matrix(c(1,1,1,1,1,1,1,1,0,0,0,0,1,1,1,1),ncol=2,byrow=FALSE) Cmatrix<-t(t(c(0,1))) Events <- EventPointer_RNASeq(AllEvents_RNASeq,Dmatrix,Cmatrix,Statistic='LogFC',PSI=TRUE) # IGV Visualization EventsTxt<-paste(system.file('extdata',package='EventPointer'),'/EventsFound_RNASeq.txt',sep='') PathGTF<-tempdir() EventPointer_RNASeq_IGV(Events,SG_RNASeq,EventsTxt,PathGTF)