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mann-whitney-u: Mann-Whitney U Test

Citations

Docstring:

Usage: qiime stats mann-whitney-u [OPTIONS]

Inputs:
  --i-distribution ARTIFACT Dist1D[Unordered | Ordered, Independent]
                                                                    [required]
  --i-against-each ARTIFACT Dist1D[Unordered | Ordered, Matched |
    Independent]                                                    [optional]
Parameters:
  --p-compare TEXT Choices('reference', 'all-pairwise')
                         The comparison that will be used to analyze the
                         input `distribution`. Either "reference" or
                         "all-pairwise" must be selected. The "reference"
                         comparison defines Group A as the reference/control
                         provided to `reference-group` (sourced from either
                         `reference_column` or `control_column`), and Group B
                         as all other groups. The "all-pairwise" comparison
                         compares all groups to all other groups. If
                         `against-each` is used, this will define Group B.
                                                                    [required]
  --p-reference-group TEXT
                         If "reference" is the selected comparison, this is
                         the column that will be used to compare all other
                         groups against.                            [optional]
  --p-alternative TEXT Choices('two-sided', 'greater', 'less')
                         The "two-sided" alternative hypothesis is that the
                         median of Group A does not equal the median of Group
                         B. The "greater" alternative hypothesis is that the
                         median of group A is greater than the median of Group
                         B. The "less" alternative hypothesis is that the
                         median of group A is less than the median of Group B.
                                                        [default: 'two-sided']
  --p-p-val-approx TEXT Choices('auto', 'exact', 'asymptotic')
                         "exact" will calculate an exact p-value for
                         distributions, "asymptotic" will use a normal
                         distribution, and "auto" will use either "exact" when
                         one of the groups has less than 8 observations and
                         there are no ties, otherwise "asymptotic".
                                                             [default: 'auto']
Outputs:
  --o-stats ARTIFACT StatsTable[Pairwise]
                         The Mann-Whitney U table for either the "reference"
                         or "all-pairwise" comparison.              [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: mann whitney pairwise
  qiime stats mann-whitney-u \
    --i-distribution refdist.qza \
    --p-compare all-pairwise \
    --i-against-each timedist.qza \
    --p-p-val-approx asymptotic \
    --o-stats stats.qza

Import:

from qiime2.plugins.stats.methods import mann_whitney_u

Docstring:

Mann-Whitney U Test



Parameters
----------
distribution : Dist1D[Unordered | Ordered, Independent]
compare : Str % Choices('reference', 'all-pairwise')
    The comparison that will be used to analyze the input `distribution`.
    Either "reference" or "all-pairwise" must be selected. The "reference"
    comparison defines Group A as the reference/control provided to
    `reference_group` (sourced from either `reference_column` or
    `control_column`), and Group B as all other groups. The "all-pairwise"
    comparison compares all groups to all other groups. If `against_each`
    is used, this will define Group B.
reference_group : Str, optional
    If "reference" is the selected comparison, this is the column that will
    be used to compare all other groups against.
against_each : Dist1D[Unordered | Ordered, Matched | Independent], optional
alternative : Str % Choices('two-sided', 'greater', 'less'), optional
    The "two-sided" alternative hypothesis is that the median of Group A
    does not equal the median of Group B. The "greater" alternative
    hypothesis is that the median of group A is greater than the median of
    Group B. The "less" alternative hypothesis is that the median of group
    A is less than the median of Group B.
p_val_approx : Str % Choices('auto', 'exact', 'asymptotic'), optional
    "exact" will calculate an exact p-value for distributions, "asymptotic"
    will use a normal distribution, and "auto" will use either "exact" when
    one of the groups has less than 8 observations and there are no ties,
    otherwise "asymptotic".

Returns
-------
stats : StatsTable[Pairwise]
    The Mann-Whitney U table for either the "reference" or "all-pairwise"
    comparison.