EventsGTFfromTrancriptomeGTF: Events .gtf from trancriptome .gtf

Description Usage Arguments Value Examples

View source: R/EventsGTFfromTrancriptomeGTF.R

Description

Finds the alternative splicing events given a reference transcriptome.

Usage

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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

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   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.