get_taxa_by_ids: Retrieve taxa by their identifiers

In jsicherman/GemmAPI: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Retrieve taxa by their identifiers

Description

Retrieve taxa by their identifiers

Usage

get_taxa_by_ids(
  taxa,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

taxa	Limits the result to entities with given identifiers. A vector of identifiers. Identifiers can be the any of the following: taxon ID scientific name common name Retrieval by ID is more efficient. Do not combine different identifiers in one query. For convenience, below is a list of officially supported taxa ID Comm.name Scient.name NcbiID 1 human Homo sapiens 9606 2 mouse Mus musculus 10090 3 rat Rattus norvegicus 10116 11 yeast Saccharomyces cerevisiae 4932 12 zebrafish Danio rerio 7955 13 fly Drosophila melanogaster 7227 14 worm Caenorhabditis elegans 6239
raw	TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised	Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file	The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite	Whether or not to overwrite if a file exists at the specified filename.

Value

A data table with the queried taxa's details.

Examples

gemma.R:::get_taxa_by_ids(c("mouse", "human"))

jsicherman/GemmAPI documentation built on Dec. 15, 2024, 8:59 a.m.