as_analyzed_format: As Analyzed MicrobiomeR Format

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

Converts a Taxmap object to the analyzed_format.

Usage

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

Details

See the MicrobiomeR_Formats documentation.

Value

A Taxmap object in the "analyzed_format".

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

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.