Docstring:
Usage: qiime feature-table rarefy [OPTIONS]
Subsample frequencies from all samples so that the sum of frequencies in
each sample is equal to sampling-depth.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be rarefied. [required]
Parameters:
--p-sampling-depth INTEGER
Range(1, None) The total frequency that each sample should be
rarefied to. Samples where the sum of frequencies is
less than the sampling depth will be not be included
in the resulting table. [required]
--p-with-replacement / --p-no-with-replacement
Rarefy with replacement by sampling from the
multinomial distribution instead of rarefying without
replacement. [default: False]
Outputs:
--o-rarefied-table ARTIFACT FeatureTable[Frequency]
The resulting rarefied feature table. [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.
Import:
from qiime2.plugins.feature_table.methods import rarefy
Docstring:
Rarefy table
Subsample frequencies from all samples so that the sum of frequencies in
each sample is equal to sampling-depth.
Parameters
----------
table : FeatureTable[Frequency]
The feature table to be rarefied.
sampling_depth : Int % Range(1, None)
The total frequency that each sample should be rarefied to. Samples
where the sum of frequencies is less than the sampling depth will be
not be included in the resulting table.
with_replacement : Bool, optional
Rarefy with replacement by sampling from the multinomial distribution
instead of rarefying without replacement.
Returns
-------
rarefied_table : FeatureTable[Frequency]
The resulting rarefied feature table.
