utr3Annotation {InPAS} | R Documentation

## 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 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")
        }

[Package InPAS version 1.18.0 Index]