EventsGTFfromTrancriptomeGTF {EventPointer} | R Documentation |
Finds the alternative splicing events given a reference transcriptome.
EventsGTFfromTrancriptomeGTF(inputFile = NULL, Transcriptome = NULL, Pathtxt = NULL, PathGTF = NULL)
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 |
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.
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)