As Analyzed MicrobiomeR Format

Converts a Taxmap object to the analyzed_format.

as_analyzed_format(
  obj,
  cols = NULL,
  groups = NULL,
  combinations = NULL,
  out_names = NULL,
  comp_func = metacoder_comp_func_1
)

Arguments

obj

An object to be converted to a Taxmap object with create_taxmap.

cols

Column names used for calc_taxon_abund. Default: NULL

groups

Group names used for compare_groups. Default: NULL

combinations

Combinations of treatments used in compare_groups. Default: NULL

out_names

Column names of the output used for calc_obs_props. Default: NULL

comp_func

A Comparison based function used in compare_groups. Default: NULL

Value

A Taxmap object in the "analyzed_format".

Details

See the MicrobiomeR_Formats documentation.

See also

is_phyloseq_format, is_raw_format, is_basic_format, is_analyzed_format, as_raw_format, as_basic_format, order_metacoder_data

compare_groups

taxonomy_table, taxon_ids

Other Formatting: MicrobiomeR_Formats, as_MicrobiomeR_format(), as_basic_format(), as_custom_format(), as_phyloseq_format(), as_raw_format(), melt_taxmap(), treatment_matrix()