get_counts: Return the relevant counts for running TaxonSampling

Description Usage Arguments Value

View source: R/get_counts.R

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

1
2
3
4
5
6
7
8
9
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:


fcampelo/TaxonSampling documentation built on Jan. 14, 2022, 9:42 p.m.