all_genes: Get all genes

In neurogenomics/orthogene: Interspecies gene mapping

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 use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
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 gorth or homologene. NOTE: To return only the most "popular" interspecies ortholog mappings, supply mthreshold=1 here AND set method="gprofiler" above. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. For more details, please see here.

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")

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.