load_species_anno_db {SeedMatchR}

Load species specific AnnotationDb

Description

Use AnnotationHub to load species-specific GTF and 2bit DNA sequences. This function currently works for human, rat, and mouse.

The function will return:

• ⁠$gtf⁠: A GRanges object containing the GTF information

• ⁠$tx.db⁠: A tx.db object made from the GTF

• ⁠$dna⁠: The 2bit DNA sequence as a DNAStringSet

Usage

load_species_anno_db(species.name, remove.na.rows = TRUE)

Arguments

species.name

Species name. Options: human, rat, mouse

remove.na.rows

Remove rows with NA in the gene_id column

Value

Species specific AnnotationDb

Examples

anno.db = load_species_anno_db("human")