utr3Annotation: extract 3'UTR from TxDb object

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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 with 7 metadata columns: feature (utr3, next.exon.gap, CDS), annotatedProximalCP (unknown, proximalCP_<coordinate>), exon (<transcript id>_<index>), transcript, gene (entrez_id), symbol, truncated (logical).

Author(s)

Jianhong Ou

Examples

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

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.