map_species {orthogene} | R Documentation

## Standardise species names

### Description

Search `gprofiler` database for species that match the input text string. Then translate to a standardised species ID.

### Usage

    map_species(
      species = NULL,
      search_cols = c("display_name", "id", "scientific_name", "taxonomy_id"),
      output_format = c("scientific_name", "id", "display_name", "taxonomy_id", "version"),
      method = c("homologene", "gprofiler", "babelgene"),
      use_local = TRUE,
      verbose = TRUE
    )

### Arguments

`species` | Species query (e.g. "human", "homo sapiens", "hapiens", or 9606). If given a list, will iterate queries for each item. Set to `NULL` to return all species.
`search_cols` | Which columns to search for `species` substring in metadata API.
`output_format` | Which column to return.
`method` | R package to 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.
`use_local` | If `TRUE` default, map_species uses a locally stored version of the species metadata table instead of pulling directly from the gprofiler API. Local version may not be fully up to date, but should suffice for most use cases.
`verbose` | Print messages.

### Value

Species ID of type `output_format`

### Examples

    ids <- map_species(species = c(
        "human", 9606, "mus musculus",
        "fly", "C elegans"
    ))

[Package orthogene version 1.0.2 Index]