parseGff: Parse gff3/gtf genome annotation

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Parse gff3/gtf genome annotation

Description

parseGff parses genome annotation file of gff3/gtf format

Usage

parseGff(aGFF)

Arguments

aGFF	.gff3/.gff/.gtf file name

Details

Due to the complex GFF3/GFF/GTF structure of different genome annotation files from different species, this function may not be always applicable for any given file. You may need to check mannually.

Value

a parsed genome annotation object, which is a list of three elements (anno.rna, anno.need, anno.frame) and can be used for annotatePAC().

See Also

[parseTxdb()] to parse a Txdb object.

Other genome annotation functions: parseGenomeAnnotation()

Examples

## parse from a gff file, and save as .rda for further use.
gff=parseGff(aGFF='Bamboo.Hic.gff')

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.