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OmicSelector: Zero-Leakage Biomarker Discovery Toolkit

Source: R/OmicSelector-package.R
OmicSelector-package.Rd

OmicSelector 2.6.0 is a toolkit for high-dimensional biomarker discovery with leakage-resistant validation, stable feature selection, within-sample panel methods, frozen-reference denoising add-ons, qPCR non-detect handling, matched-null benchmarks, and provenance-aware audit helpers.

Details

## Key Features

- **Zero Data Leakage**: All preprocessing, feature selection, and model training occurs within proper cross-validation folds via mlr3 GraphLearners.

- **Nested Cross-Validation**: Inner loop for feature selection and hyperparameter tuning, outer loop for unbiased performance estimation.

- **Stability Metrics**: Nogueira Stability Index to ensure selected features are robust across resamples, not just high accuracy.

- **Reproducibility**: renv lockfiles, Docker containers, and deterministic pipelines.

- **Panel Governance**: Group-aware resampling, provenance-floor diagnostics, identifiability gates, matched-null benchmarks, and operating-point summaries for biomarker panels evaluated with public omics data.

## Core Classes

- [OmicPipeline]: Central R6 class for creating leakage-free pipelines - [BenchmarkService]: Enforces proper nested cross-validation

## Quick Start

“`r library(OmicSelector)

# Create pipeline from data pipeline <- OmicPipeline$new( data = my_data, target = "outcome", positive = "Case" )

# Create graph learner with feature selection learner <- pipeline$create_graph_learner( filter = "anova", model = "ranger", n_features = 20 )

# Run nested CV benchmark service <- BenchmarkService$new(pipeline, outer_folds = 5, inner_folds = 3) service$add_learner(learner) result <- service$run() “`

## Philosophy

OmicSelector 2.6.0 prioritizes leakage-resistant validation, feature stability, and auditable provenance checks above raw apparent accuracy. High accuracy with unstable feature sets or strong provenance-only prediction is treated as a warning signal rather than as direct biomarker evidence.

See also

- [OmicPipeline]: Main pipeline class - [BenchmarkService]: Nested CV service

Author

Maintainer: Konrad Stawiski konrad.stawiski@umed.lodz.pl (ORCID)

Authors:

  • Marcin Kaszkowiak

  • Damian Mikulski