EventDetection_transcriptome {EventPointer} | R Documentation

## EventDetection_transcriptome

### Description

Finds all the possible alternative splicing (AS) events given a reference transcriptome. This function use parallel foreach. User must set the value of cores (by default equal to one). Moreover, it will create a .txt file with the relative information of all the AS events found. Besides, it will return a list with main information of the splicing graph of each event. This list will be used as an input in downstream functions (Get_PSI_FromTranRef, FindPrimers, and EventPointer_RNASeq_TranRef_IGV)

### Usage

    EventDetection_transcriptome(
      inputFile = NULL,
      Transcriptome = NULL,
      Pathtxt = NULL,
      cores = 1
    )

### Arguments

`inputFile` | Path to the GTF file of the reference transcriptome.
`Transcriptome` | Name of the transcriptome
`Pathtxt` | Directory to save the .txt of the events found
`cores` | Number of cores using in the parallel processing (by default = 1)

### Value

a list is returned with the following information:

ExTP1 a sparce matrix of Events x Transcripts that relates which isoform build up the path1 of each event.

ExTP2 a sparce matrix of Events x Transcripts that relates which isoform build up the path2 of each event.

ExTPRef a sparce matrix of Events x Transcripts that relates which isoform build up the pathRef of each event.

transcritnames a vector with the annotation names of the isoforms.

SG_List A list containing the information of the splicing graph of each gene.

### Examples

             PathFiles<-system.file("extdata",package="EventPointer")
             inputFile <- paste(PathFiles,"/gencode.v24.ann_2genes.gtf",sep="")
             Transcriptome <- "Gencode24_2genes"
             Pathtxt <- tempdir()

             # Run the function

             EventXtrans <- EventDetection_transcriptome(inputFile = inputFile,
                                                          Transcriptome = Transcriptome,
                                                          Pathtxt=Pathtxt,
                                                          cores=1)

[Package EventPointer version 3.0.0 Index]