all_genes {orthogene}R Documentation

Get all genes

Description

Return all known genes from a given species.

Usage

all_genes(
  species,
  method = c("gprofiler", "homologene", "babelgene"),
  ensure_filter_nas = FALSE,
  run_map_species = TRUE,
  verbose = TRUE,
  ...
)

Arguments

species

Species to get all genes for. Will first be standardised with map_species.

method

R package to to use for gene mapping: "gprofiler" (slower but more species and genes) or "homologene" (faster but fewer species and genes).

ensure_filter_nas

Perform an extra check to remove genes that are NAs of any kind.

run_map_species

Standardise species names with map_species first (Default: TRUE).

verbose

Print messages.

...

Additional arguments to be passed to gconvert when method="gprofiler".

Details

References homologeneData or gconvert.

Value

Table with all gene symbols from the given species.

Examples

genome_mouse <- all_genes(species = "mouse")
genome_human <- all_genes(species = "human")

[Package orthogene version 1.0.2 Index]