Get Gene Information — get

Retrieves gene information (e.g., Ensembl IDs, positions) for a specific species, optionally filtered by a list of user-provided gene identifiers after converting to Ensembl IDs.

Usage

get_genes(species_id, genes = NULL)

Arguments

species_id: Numeric. The ID of the desired species.
genes: A vector or list of gene identifiers to filter by. If NULL, returns the full gene table.

Value

A data frame containing gene information (from the geneInfo table). If genes are provided, the result is filtered to match the converted Ensembl IDs.

Examples

if (FALSE) { # interactive() && curl::has_internet()
# CAUTION: The human database is very large, running these examples require
# the download of the human database.

# We have gene IDs that are not commonly recognized
head(rownames(hypoxia_reads))

# Retrieve gene information for genes in our sample
# Converts to Ensembl IDs first
genes <- get_genes(species_id = 96,
                   genes = rownames(hypoxia_reads))

head(genes)

# Retrieve all genes for desired species
all_genes <- get_genes(species_id = 96)
head(all_genes)

# This is the same as running get_table(96, "geneInfo")
all(get_genes(96) == get_table(96, "geneInfo"), na.rm = TRUE)
}