EventDetection_transcriptome {EventPointer} | R Documentation |
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)
EventDetection_transcriptome( inputFile = NULL, Transcriptome = NULL, Pathtxt = NULL, cores = 1 )
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) |
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.
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)