EventDetection_transcriptome: EventDetection_transcriptome

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

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

   ## Not run: 
         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)
    
## End(Not run)

jpromeror/EventPointer documentation built on May 17, 2023, 10:29 p.m.