parse_TxDb {InPAS} | R Documentation

## Extract gene models from a TxDb object

### Description

Extract gene models from a TxDb object and annotate last 3' UTR exons and the last CDSs

### Usage

    parse_TxDb(TxDb = NULL, edb = NULL, removeScaffolds = FALSE)

### 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.

### 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 cumbersome.

### Value

A GenomicRanges::GRanges object for gene models

### Author(s)

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

    parsed_Txdb <- parse_TxDb(TxDb, edb,
                              removeScaffolds = TRUE)

[Package InPAS version 2.2.0 Index]