Transform the output of sourmash taxonomy annotate into a taxmap metacoder object

Usage

from_taxonomy_annotate_to_metacoder(
  taxonomy_annotate_df = NULL,
  file = NULL,
  intersect_bp_threshold = 50000,
  tax_glom_level = NULL,
  groups = NULL,
  groups_prefix = "x",
  class_key = NULL,
  class_regex = NULL
)

Arguments

taxonomy_annotate_df: Data frame containing outputs from sourmash taxonomy annotate. If specified, file is ignored. Can contain results from one or many runs of sourmash taxonomy annotate.
file: Path to CSV file or files output by sourmash taxonomy annotate.
intersect_bp_threshold: Integer. Gather matches must have an intersect_bp greater than or equal to this value.
tax_glom_level: Character. NULL by default, meaning no agglomeration is done. Valid options are "domain", "phylum", "class", "order", "family", "genus", and "species". When a valid option is supplied, k-mer counts are agglomerated to that level before metacoder object is created.
groups: A data frame with distinct query_name values from taxonomy_annotate_df in the first column and query groups in the second column.
groups_prefix: Character. Ignored if groups is defined. Used to prefix query_name values for the metacoder function calc_n_samples().
class_key: Character. class_key to use to build metacoder object. See metacoder documentation for more information. Ignored if you used pre-built sourmash GenBank or GTDB databases when running sourmash.
class_regex: Character. class_regex to use to build metacoder object. See metacoder documentation for more information. Ignored if you used pre-built sourmash GenBank or GTDB databases when running sourmash.

Value

A metacoder taxmap object.

Examples

if (FALSE) {
from_taxonomy_annotate_to_metacoder()
}