Docstring:
Usage: qiime composition ancombc [OPTIONS]
Apply Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-
BC) to identify features that are differentially abundant across groups.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be used for ANCOM-BC
computation. [required]
Parameters:
--m-metadata-file METADATA...
(multiple The sample metadata.
arguments will be
merged) [required]
--p-formula TEXT How the microbial absolute abundances for each taxon
depend on the variables within the `metadata`.
[required]
--p-p-adj-method TEXT Choices('holm', 'hochberg', 'hommel', 'bonferroni',
'BH', 'BY', 'fdr', 'none')
Method to adjust p-values. [default: 'holm']
--p-prv-cut NUMBER A numerical fraction between 0-1. Taxa with
prevalences less than this value will be excluded
from the analysis. [default: 0.1]
--p-lib-cut INTEGER A numerical threshold for filtering samples based on
library sizes. Samples with library sizes less than
this value will be excluded from the analysis.
[default: 0]
--p-reference-levels TEXT...
List[Str] Define the reference level(s) to be used for
categorical columns found in the `formula`. These
categorical factors are dummy coded relative to the
reference(s) provided. The syntax is as follows:
"column_name::column_value" [optional]
--p-tol NUMBER The iteration convergence tolerance for the E-M
algorithm. [default: 1e-05]
--p-max-iter INTEGER The maximum number of iterations for the E-M
algorithm. [default: 100]
--p-conserve / --p-no-conserve
Whether to use a conservative variance estimator for
the test statistic. It is recommended if the sample
size is small and/or the number of differentially
abundant taxa is believed to be large.
[default: False]
--p-alpha NUMBER Level of significance. [default: 0.05]
Outputs:
--o-differentials ARTIFACT FeatureData[DifferentialAbundance]
The calculated per-feature differentials. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Examples:
# ### example: ancombc single formula
qiime composition ancombc \
--i-table table.qza \
--m-metadata-file metadata.tsv \
--p-formula bodysite \
--o-differentials dataloaf.qza
# ### example: ancombc multi formula with reference levels
qiime composition ancombc \
--i-table table.qza \
--m-metadata-file metadata.tsv \
--p-formula 'bodysite + animal' \
--p-reference-levels bodysite::tongue animal::dog \
--o-differentials dataloaf.qza
Import:
from qiime2.plugins.composition.methods import ancombc
Docstring:
Analysis of Composition of Microbiomes with Bias Correction
Apply Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-
BC) to identify features that are differentially abundant across groups.
Parameters
----------
table : FeatureTable[Frequency]
The feature table to be used for ANCOM-BC computation.
metadata : Metadata
The sample metadata.
formula : Str
How the microbial absolute abundances for each taxon depend on the
variables within the `metadata`.
p_adj_method : Str % Choices('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'), optional
Method to adjust p-values.
prv_cut : Float, optional
A numerical fraction between 0-1. Taxa with prevalences less than this
value will be excluded from the analysis.
lib_cut : Int, optional
A numerical threshold for filtering samples based on library sizes.
Samples with library sizes less than this value will be excluded from
the analysis.
reference_levels : List[Str], optional
Define the reference level(s) to be used for categorical columns found
in the `formula`. These categorical factors are dummy coded relative to
the reference(s) provided. The syntax is as follows:
"column_name::column_value"
tol : Float, optional
The iteration convergence tolerance for the E-M algorithm.
max_iter : Int, optional
The maximum number of iterations for the E-M algorithm.
conserve : Bool, optional
Whether to use a conservative variance estimator for the test
statistic. It is recommended if the sample size is small and/or the
number of differentially abundant taxa is believed to be large.
alpha : Float, optional
Level of significance.
Returns
-------
differentials : FeatureData[DifferentialAbundance]
The calculated per-feature differentials.
