parseGenomeAnnotation: Parse genome annotation

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

Parse genome annotation

Description

parseGenomeAnnotation parses different types of genome annotations.

Usage

parseGenomeAnnotation(anAnno)

Arguments

anAnno

can be a list of anno.rna/anno.need, or .rda/.rdata/.gff3/.gtf file name, or TxDB object.

Details

Due to the complex GFF3/GTF/TxDB 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

[annotatePAC()] to annotate a PACdataset.

Other genome annotation functions: parseGff()

Examples

## Way1: Based on an annotation file in gff3 format,
## You can dowonload annotation from Ensemble Plants
#Prepare the annotation
#wget -c ftp://ftp.ensemblgenomes.org/pub/plants/release-44/gff3/
#        arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.44.gff3.gz
#gunzip  Arabidopsis_thaliana.TAIR10.44.gff3.gz
gff.path <- "/path/Arabidopsis_thaliana.TAIR10.44.gff3"
anno <- parseGenomeAnnotation(anAnno=gff.path)

##way2: load from a .rda file (already processed file)
anno <- parseGenomeAnnotation("anno.rda")

##Way3: Based on a TxDb object generated from BioMart.
# Parse Arabidopsis Txdb
library(TxDb.Athaliana.BioMart.plantsmart28)
anno <- parseGenomeAnnotation(TxDb.Athaliana.BioMart.plantsmart28)
# Parse mm10 Txdb
BiocManager::install("TxDb.Mmusculus.UCSC.mm10.ensGene")
library(TxDb.Mmusculus.UCSC.mm10.ensGene)
anno <- parseGenomeAnnotation(TxDb.Mmusculus.UCSC.mm10.ensGene)

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