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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.                    [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.