Skip to contents

Load species specific AnnotationDb

Source: R/load_species_anno_db.R
load_species_anno_db.Rd

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

if (FALSE) { # interactive()
anno.db = load_species_anno_db("human")
}