Package index • OmicSelector

Core Pipeline

Main classes for building zero-leakage ML pipelines

OmicPipeline: OmicPipeline: Zero-Leakage Feature Selection Pipeline
omic_pipeline(): Quick pipeline creation from data
BenchmarkService: BenchmarkService: Nested Cross-Validation with Zero Leakage
omic_benchmark(): Create benchmark service from OmicPipeline

Signature Selection

Multi-objective biomarker signature selection

select_best_signature(): Select Best Biomarker Signature from Nested CV Results
get_consensus_features(): Get Consensus Features from Best Signature
get_selected_features_per_fold(): Get Selected Features Per Fold

Stability Analysis

Feature selection stability metrics

compute_nogueira_stability(): Compute Nogueira Stability Index
compute_stability_from_resample(): Compute Stability from ResampleResult
extract_features_from_resample(): Extract Features from All Folds in ResampleResult
extract_selected_features(): Extract Selected Features from Trained GraphLearner

Batch Correction

FrozenComBat for proper batch effect handling

FrozenComBat: FrozenComBat R6 Class
frozen_combat_correct(): Convenience function for frozen ComBat correction
create_frozen_combat_pipeop(): Create a Frozen ComBat PipeOp for mlr3pipelines

Calibration

Probability calibration and diagnostics

fit_platt_scaling(): Platt Scaling (Logistic Calibration)
fit_isotonic_calibration(): Isotonic Regression Calibration
fit_temperature_scaling(): Temperature Scaling
compute_ece(): Compute Expected Calibration Error (ECE)
decompose_brier(): Decompose Brier Score
calibration_summary(): Calibration Summary for Model Results
reliability_diagram_data(): Create Reliability Diagram Data

Interpretability

Model interpretation and feature importance

create_explainer(): Create Model Explainer
shap_values(): Compute SHAP-like Values
feature_importance(): Compute Permutation Feature Importance
partial_dependence(): Compute Partial Dependence
check_feature_correlations(): Check Feature Correlations

Phase 5: GOF Filters

Goodness-of-fit filters for sparse/zero-inflated omics data

FilterGOF_KS: Kolmogorov-Smirnov GOF Filter
FilterHurdle: Hurdle Filter for Zero-Inflated Data
FilterZeroProp: Zero-Proportion Filter
make_gof_filter(): Create GOF Filter
compare_gof_filters(): Compare GOF Filters on Task
register_gof_filters(): Register GOF Filters in mlr3

Phase 5: Bayesian Tuning

Bayesian hyperparameter optimization with mlr3mbo

make_autotuner_glmnet(): Create Bayesian-Optimized AutoTuner for glmnet
make_autotuner_xgboost(): Create Bayesian-Optimized AutoTuner for XGBoost
make_autotuner_ranger(): Create Bayesian-Optimized AutoTuner for Random Forest
make_autotuner_lightgbm(): Create Bayesian-Optimized AutoTuner for LightGBM
get_optimal_params(): Get Optimal Hyperparameters from AutoTuner
run_bayesian_benchmark(): Run Bayesian Optimization Benchmark

Phase 5: AutoXAI

DALEX-based interpretability with correlation warnings

xai_pipeline(): Run Complete XAI Pipeline
xai_explainer_mlr3(): Create DALEX Explainer from mlr3 Learner
xai_importance(): Compute Permutation Feature Importance
xai_correlations(): Compute Correlation Diagnostics for Features
xai_pdp(): Compute Partial Dependence Plots
xai_shap(): Compute SHAP Values for Observations
plot_xai_importance(): Plot XAI Feature Importance
print_xai_summary(): Print XAI Summary

Phase 5: Stability Ensemble

Bootstrap-based feature selection stability

create_stability_ensemble(): Create a Stability Ensemble with Presets
StabilityEnsemble: Stability-Based Ensemble Selection
SequentialSelector: Hybrid Sequential Feature Selection (HSFS)

Phase 5: Synthetic Data

Data augmentation and synthetic data generation

smote_augment(): SMOTE Augmentation for Omics Data
noise_augment(): Gaussian Noise Augmentation
validate_synthetic(): Validate Synthetic Data Quality
balance_classes(): Create Balanced Training Set
tabddpm_generate(): TabDDPM Synthetic Data Generator

Phase 5: Deep Learning

Deep learning models for omics (requires torch)

create_mlp_learner(): Create MLP Learner via mlr3torch
make_mlp_learner(): Create Omics-Optimized MLP Learner
make_tabtransformer_learner(): Create TabTransformer Learner
make_gnn_learner(): Create GNN Learner for Pathway-Aware Classification
build_correlation_adjacency(): Create Correlation-Based Adjacency for GNN
run_dl_benchmark(): Deep Learning Benchmark
check_dl_availability(): Check Deep Learning Availability

Multi-Omics

Multi-omics late integration

merge_omics_data(): Merge Multi-Omics Data for Analysis
get_modality_info(): Get Modality Information
validate_omics_input(): Validate Multi-Omics Input
stack_omics(): Create Multi-Omics Stacked Ensemble (Convenience Function)

Model Export & Reporting

Model deployment and TRIPOD reporting

generate_tripod_report(): Generate TRIPOD+AI Report
create_report_data(): Create Report Data Schema

Utilities

Helper functions for parallel processing and caching

setup_parallel(): Configure Parallelization for OmicSelector
with_parallel(): With Parallel Scope
get_parallel_status(): Get Current Parallelization Status
reset_parallel(): Reset Parallelization to Sequential
create_omic_cache(): Create Split-Aware Cache
cached_filter(): Cached Filter Computation
cache_stats(): Get Cache Statistics
clear_cache(): Clear OmicSelector Cache

Legacy Functions

Functions from OmicSelector 1.x (use with caution)

list_deprecated_functions(): List all deprecated functions
OmicSelector_OmicSelector_wrapper(): OmicSelector_OmicSelector (DEPRECATED)
OmicSelector_PCA(): OmicSelector_PCA
OmicSelector_PCA_3D(): OmicSelector_PCA_3D
OmicSelector_benchmark(): OmicSelector_benchmark
OmicSelector_best_signature_de(): OmicSelector_best_signature_de
OmicSelector_best_signature_proposals(): OmicSelector_best_signature_proposals
OmicSelector_best_signature_proposals_meta11(): OmicSelector_best_signature_proposals_meta11
OmicSelector_combat(): OmicSelector_combat
OmicSelector_correct_miRNA_names(): OmicSelector_correct_miRNA_names
OmicSelector_correlation_plot(): OmicSelector_correlation_plot
OmicSelector_counts_to_log10tpm(): OmicSelector_counts_to_log10tpm
OmicSelector_create_formula(): OmicSelector_create_formula
OmicSelector_differential_expression_ttest(): OmicSelector_differential_expression_ttest
OmicSelector_diverge_color(): OmicSelector_diverge_color
OmicSelector_docker.update_progress(): OmicSelector_docker.update_progress
OmicSelector_download_tissue_miRNA_data_from_TCGA(): OmicSelector_download_tissue_miRNA_data_from_TCGA
OmicSelector_get_benchmark(): OmicSelector_get_benchmark
OmicSelector_get_benchmark_methods(): OmicSelector_get_benchmark_methods
OmicSelector_get_features_from_benchmark(): OmicSelector_get_features_from_benchmark
OmicSelector_heatmap.3(): OmicSelector_heatmap.3
OmicSelector_heatmap(): OmicSelector_heatmap
OmicSelector_iteratedRFE(): OmicSelector_iteratedRFE
OmicSelector_iteratedRFE_deprecated(): Wrapper for deprecated OmicSelector_iteratedRFE
OmicSelector_load_datamix(): OmicSelector_load_datamix
OmicSelector_load_extension(): OmicSelector_load_extension
OmicSelector_log(): OmicSelector_log
OmicSelector_merge_formulas(): OmicSelector_merge_formulas
OmicSelector_myclust(): OmicSelector_myclust
OmicSelector_mydist(): OmicSelector_mydist
OmicSelector_prepare_split(): OmicSelector_prepare_split
OmicSelector_process_tissue_miRNA_TCGA(): OmicSelector_process_tissue_miRNA_TCGA
OmicSelector_profileplot(): OmicSelector_profileplot
OmicSelector_propensity_score_matching(): OmicSelector_propensity_score_matching
OmicSelector_setup(): OmicSelector_setup
OmicSelector_signature_overlap(): OmicSelector_signature_overlap
OmicSelector_table(): OmicSelector_table
OmicSelector_vulcano_plot(): OmicSelector_vulcano_plot
OmicSelector_xgboost(): OmicSelector_xgboost

Internal Functions

Internal functions and helpers (exported for advanced use)

AutoXAI: Auto XAI: Automatic Explainability for Biomarker Models
BayesianTuner: Bayesian Hyperparameter Optimization for Omics
BenchmarkService: BenchmarkService: Nested Cross-Validation with Zero Leakage
DeepLearners: Deep Learning Learners for Omics Data
FilterGOF: Goodness-of-Fit Filters for Sparse Omics Data
FilterGOF_KS: Kolmogorov-Smirnov GOF Filter
FilterHurdle: Hurdle Filter for Zero-Inflated Data
FilterZeroProp: Zero-Proportion Filter
FrozenComBat: FrozenComBat R6 Class
OmicModalitySpec: OmicModalitySpec R6 Class
OmicPipeline: OmicPipeline: Zero-Leakage Feature Selection Pipeline
OmicSelector-package OmicSelector: OmicSelector: Zero-Leakage Biomarker Discovery Toolkit
OmicSelector_OmicSelector_wrapper(): OmicSelector_OmicSelector (DEPRECATED)
OmicSelector_PCA(): OmicSelector_PCA
OmicSelector_PCA_3D(): OmicSelector_PCA_3D
OmicSelector_benchmark(): OmicSelector_benchmark
OmicSelector_best_signature_de(): OmicSelector_best_signature_de
OmicSelector_best_signature_proposals(): OmicSelector_best_signature_proposals
OmicSelector_best_signature_proposals_meta11(): OmicSelector_best_signature_proposals_meta11
OmicSelector_combat(): OmicSelector_combat
OmicSelector_correct_miRNA_names(): OmicSelector_correct_miRNA_names
OmicSelector_correlation_plot(): OmicSelector_correlation_plot
OmicSelector_counts_to_log10tpm(): OmicSelector_counts_to_log10tpm
OmicSelector_create_formula(): OmicSelector_create_formula
OmicSelector_differential_expression_ttest(): OmicSelector_differential_expression_ttest
OmicSelector_diverge_color(): OmicSelector_diverge_color
OmicSelector_docker.update_progress(): OmicSelector_docker.update_progress
OmicSelector_download_tissue_miRNA_data_from_TCGA(): OmicSelector_download_tissue_miRNA_data_from_TCGA
OmicSelector_get_benchmark(): OmicSelector_get_benchmark
OmicSelector_get_benchmark_methods(): OmicSelector_get_benchmark_methods
OmicSelector_get_features_from_benchmark(): OmicSelector_get_features_from_benchmark
OmicSelector_heatmap.3(): OmicSelector_heatmap.3
OmicSelector_heatmap(): OmicSelector_heatmap
OmicSelector_iteratedRFE(): OmicSelector_iteratedRFE
OmicSelector_iteratedRFE_deprecated(): Wrapper for deprecated OmicSelector_iteratedRFE
OmicSelector_load_datamix(): OmicSelector_load_datamix
OmicSelector_load_extension(): OmicSelector_load_extension
OmicSelector_log(): OmicSelector_log
OmicSelector_merge_formulas(): OmicSelector_merge_formulas
OmicSelector_myclust(): OmicSelector_myclust
OmicSelector_mydist(): OmicSelector_mydist
OmicSelector_prepare_split(): OmicSelector_prepare_split
OmicSelector_process_tissue_miRNA_TCGA(): OmicSelector_process_tissue_miRNA_TCGA
OmicSelector_profileplot(): OmicSelector_profileplot
OmicSelector_propensity_score_matching(): OmicSelector_propensity_score_matching
OmicSelector_setup(): OmicSelector_setup
OmicSelector_signature_overlap(): OmicSelector_signature_overlap
OmicSelector_table(): OmicSelector_table
OmicSelector_vulcano_plot(): OmicSelector_vulcano_plot
OmicSelector_xgboost(): OmicSelector_xgboost
OmicStackedEnsemble: OmicStackedEnsemble R6 Class
OmicWeightedEnsemble: Simple Weighted Averaging Ensemble
SequentialSelector: Hybrid Sequential Feature Selection (HSFS)
StabilityEnsemble: Stability-Based Ensemble Selection
SyntheticData: Synthetic Data Generation for Omics
apply_frozen_combat_cv(): Apply Frozen ComBat Within Cross-Validation Folds
balance_classes(): Create Balanced Training Set
build_correlation_adjacency(): Create Correlation-Based Adjacency for GNN
cache: Split-Aware Caching for OmicSelector 2.0
cache_stats(): Get Cache Statistics
cached_filter(): Cached Filter Computation
calibration: Calibration Metrics for OmicSelector 2.0
calibration_summary(): Calibration Summary for Model Results
check_batch_correction_leakage(): Check for Batch Correction Leakage
check_dl_availability(): Check Deep Learning Availability
check_feature_correlations(): Check Feature Correlations
clear_cache(): Clear OmicSelector Cache
compare_gof_filters(): Compare GOF Filters on Task
compute_ece(): Compute Expected Calibration Error (ECE)
compute_nogueira_stability(): Compute Nogueira Stability Index
compute_shap_with_warnings(): Compute SHAP Values with Correlation Warnings
compute_stability_from_resample(): Compute Stability from ResampleResult
create_explainer(): Create Model Explainer
create_frozen_combat_pipeop(): Create a Frozen ComBat PipeOp for mlr3pipelines
create_hsfs_selector(): Create a Hybrid Sequential Feature Selector
create_mlp_learner(): Create MLP Learner via mlr3torch
create_omic_cache(): Create Split-Aware Cache
create_report_data(): Create Report Data Schema
create_stability_ensemble(): Create a Stability Ensemble with Presets
decompose_brier(): Decompose Brier Score
deprecated: Deprecated and Leaky Functions
export_bundle(): Create Complete Export Bundle
export_onnx(): Export Model to ONNX Format
export_vetiver(): Export Model as Vetiver for Deployment
extract_features_from_resample(): Extract Features from All Folds in ResampleResult
extract_selected_features(): Extract Selected Features from Trained GraphLearner
feature_importance(): Compute Permutation Feature Importance
fit_isotonic_calibration(): Isotonic Regression Calibration
fit_platt_scaling(): Platt Scaling (Logistic Calibration)
fit_temperature_scaling(): Temperature Scaling
frozen-combat: Frozen ComBat for Leakage-Free Batch Correction
frozen_combat_correct(): Convenience function for frozen ComBat correction
generate_cache_key(): Generate Split-Aware Cache Key
generate_tripod_report(): Generate TRIPOD+AI Report
get_consensus_features(): Get Consensus Features from Best Signature
get_modality_info(): Get Modality Information
get_optimal_params(): Get Optimal Hyperparameters from AutoTuner
get_parallel_status(): Get Current Parallelization Status
get_reliable_shap_features(): Get Reliable SHAP Features
get_selected_features_per_fold(): Get Selected Features Per Fold
interpretability: Model Interpretability for OmicSelector 2.0
list_deprecated_functions(): List all deprecated functions
load_bundle(): Load Exported Model Bundle
make_autotuner_glmnet(): Create Bayesian-Optimized AutoTuner for glmnet
make_autotuner_lightgbm(): Create Bayesian-Optimized AutoTuner for LightGBM
make_autotuner_ranger(): Create Bayesian-Optimized AutoTuner for Random Forest
make_autotuner_xgboost(): Create Bayesian-Optimized AutoTuner for XGBoost
make_gnn_learner(): Create GNN Learner for Pathway-Aware Classification
make_gof_filter(): Create GOF Filter
make_mlp_learner(): Create Omics-Optimized MLP Learner
make_tabtransformer_learner(): Create TabTransformer Learner
memoize_with_split(): Memoize Function with Split Context
merge_omics_data(): Merge Multi-Omics Data for Analysis
model-export: Model Export for OmicSelector 2.0
multi-omics: Multi-Omics Support for OmicSelector 2.0
noise_augment(): Gaussian Noise Augmentation
omic_benchmark(): Create benchmark service from OmicPipeline
omic_pipeline(): Quick pipeline creation from data
parallel: Parallelization Support for OmicSelector 2.0
partial_dependence(): Compute Partial Dependence
plot_signature_tradeoffs(): Plot Signature Selection Trade-offs
plot_xai_importance(): Plot XAI Feature Importance
print(<CalibrationResult>): Print method for CalibrationResult
print(<CorrelationCheck>): Print Correlation Check
print(<FeatureImportance>): Print Feature Importance
print(<LeakageValidation>): Print method for LeakageValidation
print(<NestedCVResult>): Print method for NestedCVResult
print(<NogueiraStability>): Print method for NogueiraStability
print(<OmicBenchmarkResult>): Print method for OmicBenchmarkResult
print(<OmicsInput>): Print method for OmicsInput
print(<ReportData>): Print method for ReportData
print(<SignatureSelectionResult>): Print Method for Signature Selection Result
print_shap_warnings(): Print SHAP Warnings Report
print_xai_summary(): Print XAI Summary
register_gof_filters(): Register GOF Filters in mlr3
reliability_diagram_data(): Create Reliability Diagram Data
report: TRIPOD+AI Report Generation for OmicSelector 2.0
reset_parallel(): Reset Parallelization to Sequential
run_bayesian_benchmark(): Run Bayesian Optimization Benchmark
run_dl_benchmark(): Deep Learning Benchmark
select_best_signature(): Select Best Biomarker Signature from Nested CV Results
setup_parallel(): Configure Parallelization for OmicSelector
shap_values(): Compute SHAP-like Values
shap_warnings: Correlation-Aware SHAP Interpretation
signature-selection: Signature Selection: Multi-Objective Best Biomarker Selection
smote_augment(): SMOTE Augmentation for Omics Data
stability: Nogueira Stability Index for Feature Selection
stack_omics(): Create Multi-Omics Stacked Ensemble (Convenience Function)
tabddpm_generate(): TabDDPM Synthetic Data Generator
torch-learners: mlr3torch Learner Integration for OmicSelector 2.0
validate_no_leakage(): Validate pipeline for leakage risks
validate_omics_input(): Validate Multi-Omics Input
validate_synthetic(): Validate Synthetic Data Quality
with_parallel(): With Parallel Scope
xai_correlations(): Compute Correlation Diagnostics for Features
xai_explainer_mlr3(): Create DALEX Explainer from mlr3 Learner
xai_importance(): Compute Permutation Feature Importance
xai_pdp(): Compute Partial Dependence Plots
xai_pipeline(): Run Complete XAI Pipeline
xai_shap(): Compute SHAP Values for Observations