EventPointer_RNASeq_TranRef_IGV: EventPointer RNASeq from reference transcriptome IGV...

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

EventPointer RNASeq from reference transcriptome IGV Visualization

Description

Generates of files to be loaded in IGV for visualization and interpretation of events detected from a reference transcriptome (see EventDetection_transcriptome).

Usage

EventPointer_RNASeq_TranRef_IGV(SG_List, pathtoeventstable, PathGTF)

Arguments

SG_List	List with the Splicing Graph information of the events. This list is created by EventDetection_transcriptome function.
pathtoeventstable	Complete path to the table returned by EventDetection_transcriptome that contains the information of each event, or table with specific events that the user want to load into IGV to visualize.
PathGTF	Directory where to write the GTF files.

Value

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 is named 'paths_RNASeq.gtf'.

Examples

  ###### example using all the events found in a reference transcriptome
  data("EventXtrans")
  SG_List <- EventXtrans$SG_List
  PathEventsTxt<-system.file('extdata',package='EventPointer')
  PathEventsTxt <- paste0(PathEventsTxt,"/EventsFound_Gencode24_2genes.txt")
  PathGTF <- tempdir()
  
  EventPointer_RNASeq_TranRef_IGV(SG_List = SG_List,pathtoeventstable = PathEventsTxt,PathGTF = PathGTF)
  
  
     

jpromeror/EventPointer documentation built on May 17, 2023, 10:29 p.m.