InPAS (version 1.4.4)

utr3Annotation: extract 3'UTR from TxDb object

Description

extract 3'UTR from a TxDb object. The 3'UTR is defined as the last 3'UTR fragment for each transcript and it will be cut if there is any overlaps with other exons.

Usage

utr3Annotation(txdb, orgDbSYMBOL, MAX_EXONS_GAP = 10000)

Arguments

txdb

an object of TxDb

orgDbSYMBOL

a string indicates org SYMBOL to entriz id map

MAX_EXONS_GAP

maximul exon gap for distal CP site

Value

return an object of GRanges

Examples

    if(interactive()){
        library(TxDb.Mmusculus.UCSC.mm10.knownGene)
    
        library(org.Mm.eg.db)
        
        utr3Annotation(TxDb.Mmusculus.UCSC.mm10.knownGene, "org.Mm.egSYMBOL")
    }