xref_taxonomy_number: Cross reference the taxonomy data from GenomeInfoDb with...

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

Cross reference the taxonomy data from GenomeInfoDb with EuPathDB metadata.

Description

Previously this tried to set species and taxonomy number, but I am having it only do the number now in the hopes that it simplifies things somewhat.

Usage

xref_taxonomy_number(
  metadatum,
  all_taxa_ids,
  verbose = FALSE,
  taxon_number_column = "TaxonomyID",
  metadata_taxon_column = "TaxonUnmodified"
)

Arguments

verbose	Print some information about what is found as this runs?
metadata	Information provided by downloading the metadata from a eupathdb sub project.
species_column	Because the species column name has changed.
taxon_column	Because the taxonomy column name has changed.

Value

List containing entries which pass and fail after xrefing against loadTaxonomyDb().

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