Difference between contingency filtering and both of feature and sample filterings?

[Mehrdad (Meha)]

What makes the filtering modes difference while their parameters are the same?

https://docs.qiime2.org/2019.1/tutorials/filtering/#taxonomy-based-filtering-of-tables-and-sequences

[Mehrdad (Meha)]

in a nutshell, I do not understand difference between max/min (sample or feature) and max/min frequencies! could you please tell me the difference? I think they are same!

[Nicholas_Bokulich]

filter-samples filters out samples. filter-features filters out features. So while the parameters may sound similar, they operate on different axes. I recommend reading the help documentation to learn more:

$ qiime feature-table filter-features --help
Usage: qiime feature-table filter-features [OPTIONS]

  Filter features from table based on frequency and/or metadata. Any samples
  with a frequency of zero after feature filtering will also be removed. See
  the filtering tutorial on https://docs.qiime2.org for additional details.

Options:
  --p-min-frequency INTEGER       The minimum total frequency that a feature
                                  must have to be retained.  [default: 0]
  --p-max-frequency INTEGER       The maximum total frequency that a feature
                                  can have to be retained. If no value is
                                  provided this will default to infinity
                                  (i.e., no maximum frequency filter will be
                                  applied).  [optional]
  --p-min-samples INTEGER         The minimum number of samples that a feature
                                  must be observed in to be retained.
                                  [default: 0]
  --p-max-samples INTEGER         The maximum number of samples that a feature
                                  can be observed in to be retained. If no
                                  value is provided this will default to
                                  infinity (i.e., no maximum sample filter
                                  will be applied).  [optional]

$ qiime feature-table filter-samples --help
Usage: qiime feature-table filter-samples [OPTIONS]

  Filter samples from table based on frequency and/or metadata. Any features
  with a frequency of zero after sample filtering will also be removed. See
  the filtering tutorial on https://docs.qiime2.org for additional details.

Options:
  --p-min-frequency INTEGER       The minimum total frequency that a sample
                                  must have to be retained.  [default: 0]
  --p-max-frequency INTEGER       The maximum total frequency that a sample
                                  can have to be retained. If no value is
                                  provided this will default to infinity
                                  (i.e., no maximum frequency filter will be
                                  applied).  [optional]
  --p-min-features INTEGER        The minimum number of features that a sample
                                  must have to be retained.  [default: 0]
  --p-max-features INTEGER        The maximum number of features that a sample
                                  can have to be retained. If no value is
                                  provided this will default to infinity
                                  (i.e., no maximum feature filter will be
                                  applied).  [optional]