get_counts: Return the relevant counts for running TaxonSampling

In fcampelo/TaxonSampling: Hierarchical Taxonomic Sampling for Maximized Diversity at All Levels

Description

This function evaluates the taxonomical structure from a set of input IDs and returns the count of each taxon ID with non-zero occurrences in the taxonomy graph, as well as the count of known species under each taxon.

Usage

get_counts(
  taxonomy_path,
  ids_file = NULL,
  ids_df = NULL,
  spp_file = NULL,
  spp_df = NULL,
  start_from_species = FALSE,
  verbose = TRUE
)

Arguments

taxonomy_path	path to folder containing the NCBI taxonomy files (i.e., the extracted contents of _taxdump.zip_, which can be downloaded from <ftp://ftp.ncbi.nih.gov/pub/taxonomy/> or retrieved using [retrieve_NCBI_taxonomy()]).
ids_file	path to a tab-separated file containng two two columns, with the input taxon IDs in the first column, and the corresponding sequence IDs (corresponding to the ID strings int the multifasta input file, without the ">" line starter) in the second column.
ids_df	two-column data frame with the input taxon IDs in the first column, and the corresponding sequence IDs (corresponding to the ID strings int the multifasta input file, without the ">" line starter) in the second column. Ignored if 'ids_file' is not 'NULL'.
spp_file	path to a tab-separated file containing two two columns, with the input taxon IDs in the first column, and the corresponding number of known species in the second column. If both 'spp_file' and 'spp_df' are 'NULL', then the counts are computed internally based either on the taxonomy files under 'taxonomy_path'.
spp_df	two-column data frame with the input taxon IDs in the first column, and the corresponding number of known species in the second column. This can be generated using [get_taxID_spp_counts()]. Ignored if 'spp_file' is not 'NULL'.
start_from_species	logical, passed down to [get_taxID_spp_counts()] (only if 'spp_file' and 'spp_file' are 'NULL').
verbose	logical: regulates function echoing to console.

Value

list object of class _taxonsampling_, containing:

• '$ids_df': data.frame with taxon IDs in column 1 and corresponding sequence IDs in column 2, as loaded from 'ids_file' or passed directly as input. Filtered to maintain only IDs that exist in '$nodes' and to remove duplicated IDs.

• '$nodes': data.frame containing the pre-processed information about the NCBI taxonomy structure, extracted from file _nodes.dmp_ of the taxonomy files. Filtered to keep only nodes with IDs present in '$ids_df' and with a non-zero total count.

• '$countIDs': numeric vector with the counts of the number of taxonomy nodes (of all levels) under each taxon ID.

• 'spp_df': two-column data frame with the input taxon IDs in the first column, and the corresponding number of known species in the second column. Filtered to have only the IDs present in '$countIDs'.

fcampelo/TaxonSampling documentation built on Jan. 29, 2022, 7:11 a.m.