get_eupath_entry: Search the eupathdb metadata for a given species substring.

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Search the eupathdb metadata for a given species substring.

Description

When querying the eupathdb, it can be difficult to hit the desired species. This is confounded by the fact that there are very similar named species across different EupathDB projects. Thus function seeks to make it a bit easier to find the actual dataset desired. If the specific species is not found, look for a reasonable approximation. stop() if nothing is found.

Usage

get_eupath_entry(
  species = "Leishmania major",
  webservice = "eupathdb",
  column = "TaxonUnmodified",
  metadata = NULL,
  ...
)

Arguments

species	String containing some reasonably unique text in the desired species name.
webservice	The EuPathDB webservice to query.
column	Which column to use for getting the species name?
metadata	Optional dataframe of already downloaded metadata.
...	Parameters passed to download_eupath_metadata()

Value

A single row from the eupathdb metadata.

Author(s)

atb

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.