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rarefy: Rarefy table

Citations
  • Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, and Rob Knight. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome, 5(1):27, Mar 2017. doi:10.1186/s40168-017-0237-y.

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 unless subsampling is performed
                       with replacement.                            [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).
  --citations          Show citations and exit.
  --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 unless subsampling is performed
    with replacement.
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.