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 2.0.0 Index]