xref_ah_species: Cross reference the taxonomy data from...

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

Cross reference the taxonomy data from AnnotationHubData::getSpeciesList()

Description

Previously, the logic of this function resided in download_eupath_metadata(), but I want to be able to test and poke at it separately to more effectively ensure as many taxa as possible pass. Therefore, I split it into its own function. The secondary function of this is to set the 'Species' column as appropriately as possible.

Usage

xref_ah_species(
  metadatum,
  ah_species,
  verbose = FALSE,
  metadata_taxon_column = "TaxonUnmodified",
  metadata_species_column = "GenusSpecies",
  gidb_species_column = "GIDB_Genus_Species",
  xref_column = "TaxonXref"
)

Arguments

verbose	Print some information about what is found?
valid	Dataframe of entries which have thus far been deemed 'valid' by my tests.
invalid	Dataframe of entries which failed.
taxon_column	metadata column with the taxonomy information.
species_column	metadata column with my generated species name.

Value

Likely smaller data frame of valid information and larger dataframe of invalid.

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