extract_UTR3Anno {InPAS} | R Documentation

## extract 3' UTR information from a GenomicFeatures::TxDb object

### Description

extract 3' UTR information from a GenomicFeatures::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

    extract_UTR3Anno(
      TxDb = NULL,
      edb = NULL,
      removeScaffolds = FALSE,
      MAX_EXONS_GAP = 10000
    )

### Arguments

`TxDb` | an object of GenomicFeatures::TxDb
`edb` | An object of ensembldb::EnsDb
`removeScaffolds` | A logical(1) vector, whether the scaffolds should be removed from the genome If you use a TxDb containing alternative scaffolds, you'd better to remove the scaffolds.
`MAX_EXONS_GAP` | An integer(1) vector, maximal gap sizes between last known CP sites to downstream exons

### Details

A good practice is to perform read alignment using a reference genome from Ensembl/GenCode including only the primary assembly and build a TxDb using the GTF/GFF files downloaded from the same source as the reference genome, such as BioMart/Ensembl/GenCode. For instruction, see Vignette of the GenomicFeatures. The UCSC reference genomes and their annotation can be very cubersome.

### Value

An object of GenomicRanges::GRangesList, containing GRanges for extracted 3' UTRs, and the corresponding last CDSs and next.exon.gap for each chromosome/scaffold.

### Author(s)

Jianhong Ou, Haibo Liu

### Examples

    library("EnsDb.Hsapiens.v86")
    library("GenomicFeatures")
    samplefile <- system.file("extdata",
                              "hg19_knownGene_sample.sqlite",
                               package = "GenomicFeatures")
    TxDb <- loadDb(samplefile)
    edb <- EnsDb.Hsapiens.v86
    utr3 <- extract_UTR3Anno(TxDb, edb,
                     removeScaffolds = TRUE,
                     MAX_EXONS_GAP = 10000)

[Package InPAS version 2.2.0 Index]