EventsGTFfromTrancriptomeGTF {EventPointer}R Documentation

Events .gtf from trancriptome .gtf

Description

Events .gtf from trancriptome .gtf

Usage

EventsGTFfromTrancriptomeGTF(inputFile = NULL, Transcriptome = NULL,
  Pathtxt = NULL, PathGTF = NULL)

Arguments

inputFile

If input is GTF, inputFile should point to the GTF file to be used.

Transcriptome

the name of the transcriptome

Pathtxt

Directory to save the .txt of the events founded

PathGTF

Directory where the output will be saved

Value

a list containing four elements: three sparce matrices that relate which isoforms build up the paths (path1,path2 and pathRef) of each event. The fourth element contains the name of the reference annotation: only appear the name of the transcript.

Examples

   PathFiles<-system.file("extdata",package="EventPointer")
   inputFile <- paste(PathFiles,"/gencode.v24.ann_2genes.gtf",sep="")
   Transcriptome <- "Gencode24_2genes"
   Pathtxt <- tempdir()
   PathGTF <- tempdir()
   
   # Run the function 
   
   EventXtrans <- EventsGTFfromTrancriptomeGTF(inputFile = inputFile,
                                               Transcriptome = Transcriptome,
                                               Pathtxt=Pathtxt,PathGTF=PathGTF)



[Package EventPointer version 2.0.1 Index]