Fork me on GitHub

first-differences: Compute first differences or difference from baseline between sequential statesΒΆ

Docstring:

Usage: qiime longitudinal first-differences [OPTIONS]

  Calculates first differences in "metric" between sequential states for
  samples collected from individual subjects sampled repeatedly at two or
  more states. First differences can be performed on a metadata column
  (including artifacts that can be input as metadata) or a feature in a
  feature table. Outputs a data series of first differences for each
  individual subject at each sequential pair of states, labeled by the
  SampleID of the second state (e.g., paired differences between time 0 and
  time 1 would be labeled by the SampleIDs at time 1). This file can be used
  as input to linear mixed effects models or other longitudinal or diversity
  methods to compare changes in first differences across time or among
  groups of subjects. Also supports differences from baseline (or other
  static comparison state) by setting the "baseline" parameter.

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                         Feature table to optionally use for computing first
                         differences.                               [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata file containing
     arguments will be   individual-id-column.
     merged)                                                        [required]
  --p-state-column TEXT  Metadata column containing state (time) variable
                         information.                               [required]
  --p-individual-id-column TEXT
                         Metadata column containing IDs for individual
                         subjects.                                  [required]
  --p-metric TEXT        Numerical metadata or artifact column to test.
                                                                    [required]
  --p-replicate-handling TEXT Choices('error', 'random', 'drop')
                         Choose how replicate samples are handled. If
                         replicates are detected, "error" causes method to
                         fail; "drop" will discard all replicated samples;
                         "random" chooses one representative at random from
                         among replicates.                  [default: 'error']
  --p-baseline NUMBER    A value listed in the state-column metadata column
                         against which all other states should be compared.
                         Toggles calculation of static differences instead of
                         first differences (which are calculated if no value
                         is given for baseline). If a "baseline" value is
                         provided, sample differences at each state are
                         compared against the baseline state, instead of the
                         previous state. Must be a value listed in the
                         state-column.                              [optional]
Outputs:
  --o-first-differences ARTIFACT SampleData[FirstDifferences]
                         Series of first differences.               [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.longitudinal.methods import first_differences

Docstring:

Compute first differences or difference from baseline between sequential
states

Calculates first differences in "metric" between sequential states for
samples collected from individual subjects sampled repeatedly at two or
more states. First differences can be performed on a metadata column
(including artifacts that can be input as metadata) or a feature in a
feature table. Outputs a data series of first differences for each
individual subject at each sequential pair of states, labeled by the
SampleID of the second state (e.g., paired differences between time 0 and
time 1 would be labeled by the SampleIDs at time 1). This file can be used
as input to linear mixed effects models or other longitudinal or diversity
methods to compare changes in first differences across time or among groups
of subjects. Also supports differences from baseline (or other static
comparison state) by setting the "baseline" parameter.

Parameters
----------
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
metric : Str
    Numerical metadata or artifact column to test.
replicate_handling : Str % Choices('error', 'random', 'drop'), optional
    Choose how replicate samples are handled. If replicates are detected,
    "error" causes method to fail; "drop" will discard all replicated
    samples; "random" chooses one representative at random from among
    replicates.
baseline : Float, optional
    A value listed in the state_column metadata column against which all
    other states should be compared. Toggles calculation of static
    differences instead of first differences (which are calculated if no
    value is given for baseline). If a "baseline" value is provided, sample
    differences at each state are compared against the baseline state,
    instead of the previous state. Must be a value listed in the
    state_column.
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for computing first differences.

Returns
-------
first_differences : SampleData[FirstDifferences]
    Series of first differences.