utr3Annotation: extract 3'UTR from TxDb object

Description Usage Arguments Value Author(s) Examples

View source: R/utr3Annotation.R

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

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    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

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    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 April 29, 2020, 5:19 a.m.