TSENATAnalysis S4 Class Definition

Central container for unified analysis workflows in TSENAT.

Usage

# S4 method for class 'TSENATAnalysis,ANY,ANY,ANY'
x[i, j, drop = TRUE]

Arguments

x

A TSENATAnalysis object to subset.

i

Gene indices (numeric, logical, or character vector). Defaults to all genes.

j

Sample indices (numeric, logical, or character vector). Defaults to all samples.

drop

Ignored for TSENATAnalysis objects; included for S4 method signature compatibility.

Value

A new TSENATAnalysis object containing only the specified genes and samples, with all associated results and metadata preserved.

Details

The TSENATAnalysis class encapsulates all components of a complete TSENAT analysis: raw data, configuration metadata, and results from each analytical step. This unified object ensures metadata is never lost through the analysis pipeline and provides consistent accessor methods for result retrieval.

Access results via the unified results(obj, type = ...) accessor method: - type='diversity' for Tsallis entropy across q-values - type='lm' for linear model interaction results - type='rank_test' for Scheirer-Ray-Hare rank-based test results - type='divergence' for divergence metrics - type='jackknife' for jackknife resampling results Use metadata(obj) to access reproducibility metadata.

Slots

se

SummarizedExperiment. The base expression data object (genes x samples) with assays and colData.

config

list. Configuration metadata specifying analysis parameters that persist through the workflow (q-values, sample grouping columns, etc.). Set once via TSENAT_config() and used by all downstream wrapper functions.

diversity_results

list. Named list of diversity calculation results. Each name corresponds to a q-value (e.g., 'q_0.5', 'q_1.0'). Values are SummarizedExperiment objects or data.frames containing entropy values for each gene at that q-value.

lm_results

list. Complex results from linear model and statistical testing. Top-level names identify analysis type:

lm_interaction

LM/GAM/GEE model results (list with $results data.frame, $models list, etc.)

rank_test

Scheirer-Ray-Hare rank-based test results

divergence_difference

Differential divergence comparison

pairwise_results

list. Pairwise group comparison results. Results from running statistical tests for group comparisons.

rank_test_results

list. Scheirer-Ray-Hare rank-based statistical test results. Names correspond to q-values (e.g., 'q_0.5', 'q_1.0'). Computed by calculate_srh() as a non-parametric alternative to linear mixed model testing.

jackknife_results

list. Resampling-based confidence intervals. Names correspond to q-values (e.g., 'q_0.5', 'q_1.0'). Values are jackknife result objects containing resamples, CI bounds, and diagnostics.

divergence_results

list. Divergence metric calculations. Typically contains:

tsallis_divergence

SummarizedExperiment with divergence values

effect_sizes

data.frame with Cohen's d, etc.

plots

list. Cached visualization objects (ggplot). Names identify plot type (e.g., 'q_curve', 'lm_interaction', 'influence'). Populated by TSENAT() if generate_plots=TRUE.

metadata

list. Reproducibility and tracking metadata. Automatically maintained by wrapper functions. Includes:

created_at

Timestamp of object creation

function_calls

Vector of wrapper functions called

function_timestamps

Timestamps for each function call

package_version

TSENAT version at creation