ref_load: Load reference annotation into a TxDb format

In dzhang32/dasper: Detecting abberant splicing events from RNA-sequencing data

Load reference annotation into a TxDb format

Description

⁠ref_load`` loads reference annotation using [makeTxDbFromGFF][GenomicFeatures::makeTxDbFromGFF] if a character or leaves ⁠ref' unchanged if already a TxDb-class. If you would

Usage

ref_load(ref)

Arguments

ref	either path to gtf/gff3 or object of class TxDb-class or EnsDb-class. EnsDb-class is required if you intend to annotate junctions with gene symbols/names.

Value

a TxDb-class object.

Examples

# create a TxDb,
ref <- GenomicState::GenomicStateHub(
    version = "31",
    genome = "hg38",
    filetype = "TxDb"
)[[1]]

# alternatively ref can be a character specifying a path to a GTF file
ref <- ref_load(ref)

dzhang32/dasper documentation built on Dec. 14, 2024, 8:33 p.m.