EventsGTFfromTrancriptomeGTF: Events .gtf from trancriptome .gtf

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

Description

Finds the alternative splicing events given a reference transcriptome.

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 five 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. The final element is SG_List: a list with the information of the graph of each gene, this variable is necesary for Primers design step.

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)

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