EventsGTFfromTrancriptomeGTF {EventPointer} | R Documentation

## Events .gtf from trancriptome .gtf

### 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)

[Package EventPointer version 2.4.0 Index]