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 `NA`s 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]