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.