Package index • GLOWr

All functions
`ALS_snvs_B_training`	ALS SNVs for B Parameter Training
`BMD_snvs_B_training`	BMD SNVs for B Parameter Training
`GLOW_Burden()`	GLOW Burden Test with Optimal Weights
`GLOW_Fisher()`	GLOW Fisher Test with Optimal Weights
`GLOW_Omni()`	GLOW Omnibus Test Combining Burden, SKAT, and Fisher
`GLOW_Omni_byP()`	GLOW Omnibus Test from Pre-Computed P-values
`GLOW_SKAT()`	GLOW SKAT Test with Optimal Weights
`Optimal_Weights_M()`	Calculate Optimal Weights for GLOW Tests
`aggregate_B_PI()`	Aggregate B and PI Vectors After Collapsing
`annotate_favor()`	Annotate Variants with FAVOR Database Scores
`annotate_gds_marginal()`	Write Marginal Analysis Results to GDS Annotation Node
`annotation_predicate()`	Build an Annotation Predicate for Variant Filtering
`apply_qc_filters()`	Apply Quality Control Filters to GWAS Data
`as.data.frame(<glow_test_result>)`	Convert GLOW Test Results to Data Frame
`assemble_pheno_covar()`	Assemble a phenotype/covariate analysis bundle
`build_variant_index()`	Build a Variant Index of a GDS for Fast Region Lookup
`calibrate_pvalues()`	Calibrate p-values by a Scalar Genomic-Control Factor
`clear_glow_cache()`	Clear GLOW Covariance Cache
`coding_filter()`	Create a Predefined Coding Category Filter
`collapse_rare_variants()`	Collapse Ultra-Rare Variants
`compare_B_models()`	Compare All Candidate Models for B Estimation
`compute_annotation_medians()`	Compute Chromosome-Wide Annotation Medians
`compute_lambda_gc()`	Genomic-Control Inflation Factor (lambda_GC)
`compute_ld_scores()`	In-sample LD Scores for One Chromosome
`compute_pcs_gds()`	Compute Principal Components from GDS Genotype Data
`compute_score_stats()`	Compute Marginal Score Statistics
`count_index_records()`	Count the Records of a Variant Index Inside Genomic Spans
`default_test_specs()`	Default Test Specifications for GLOW Omnibus Test
`define_regions_custom()`	Define Custom Genomic Regions
`define_regions_gene()`	Define Gene-Based Genomic Regions
`define_regions_noncoding()`	Define Gene-Centric Non-Coding Regions for One Chromosome and Mask
`define_regions_window()`	Define Sliding Window Regions
`detect_B_outliers()`	Detect Outliers in Training Data for B Estimation
`estimate_inflation_factor()`	Estimate the Single-Variant Inflation Factor from a Scan
`evaluate_PI_models()`	Evaluate PI Model Performance
`extract_pheno_covar_gds()`	Extract Phenotype and Covariates from GDS File
`extract_variant_set()`	Extract Filtered Variant Set from GDS
`filter_variants_ld()`	Filter Variants by Linkage Disequilibrium and Linear Dependence
`fit_null_model()`	Fit Null Model for Efficient Repeated Score Calculations
`flip_alleles()`	Flip Genotype Dosage to Minor Allele Coding
`getZ_marg_score()`	Get Standardized Marginal Score Statistics
`getZ_marg_score_binary_SPA()`	Get SPA-Adjusted Standardized Marginal Score Statistics for Binary Traits
`get_B()`	Estimate Effect Sizes (B) for Variants Based on MAF
`get_B_advanced()`	Advanced Interface for B Estimation with Full Control
`get_B_auto()`	Simplified Interface for B Estimation with Auto-Detection
`get_B_diagnostics()`	Generate Comprehensive Diagnostics for B Estimation
`get_PI()`	Estimate Variant-Importance Scores from Functional Annotations
`get_PI_train`	PI Model Training Functions
`get_PI_utils`	PI Model Utility Functions
`glow_cache_info()`	Get GLOW Cache Information
`glow_drilldown_df()`	Build a Per-Variant Drill-down Data Frame from a Region Evidence Packet
`glow_family_of()`	Classify GLOW Test Names into Test Families
`glow_region_test()`	Run the GLOW Test on a Single Genomic Region
`glow_test()`	Run GLOW Variant-Set Tests
`group_glow_tests_by_family()`	Group GLOW Test Names into a Named List of Families
`impute_na_median()`	Impute NA Values with Column Median
`ldsc_regression()`	LD Score Regression: Confounding vs Polygenicity
`load_B_model()`	Load a Trained B Estimation Model
`load_PI_models()`	Load PI Models from Directory
`load_case_annotations()`	Load Case Annotations from CSV
`load_control_annotations()`	Load Control Annotations from CSV or GDS
`marginal_scan()`	Marginal Single-Variant Association Scan
`model_PI()`	Generate Multiple PI Models
`noncoding_filter()`	The Per-Set Filter of a Gene-Centric Non-Coding Mask
`noncoding_masks()`	The Names of the Eight Gene-Centric Non-Coding Masks
`plink_to_gds()`	Convert PLINK Binary Files to GDS Format
`plot(<glow_B_estimate>)`	Plot Method for B Estimation Results
`plot(<glow_B_model>)`	Plot Method for B Estimation Models
`plot(<glow_marginal_scan>)`	Plot Method for Marginal Scan Results
`plot(<glow_pcs>)`	Plot Method for glow_pcs Objects
`plot_PI_coefficient_summary()`	Plot PI Coefficient Summary
`plot_PI_roc()`	Plot ROC Curves for PI Models
`plot_manhattan()`	Manhattan Plot for Marginal Analysis Results
`plot_qq()`	QQ Plot for Marginal Analysis P-values
`predict_B()`	Predict B Values from a Trained Model
`predict_PI_ensemble()`	Predict PI Using Ensemble of Models
`prepare_B_training_data()`	Prepare User GWAS Summary Statistics for B Estimation (ENHANCED)
`prepare_PI_case_data()`	Prepare Case Variant List for PI Estimation Training
`prepare_PI_control_data()`	Prepare Control Variant List for PI Estimation Training
`prepare_glow_input()`	Prepare Data for GLOW Testing
`print(<glow_B_diagnostics>)`	Print Method for B Diagnostics
`print(<glow_B_estimate>)`	Print Method for glow_B_estimate Objects
`print(<glow_B_model>)`	Print Method for glow_B_model Objects
`print(<glow_annotation_predicate>)`	Print Method for Annotation Predicates
`print(<glow_input>)`	Print Method for glow_input Objects
`print(<glow_outliers>)`	Print Method for glow_outliers Objects
`print(<glow_pcs>)`	Print Method for glow_pcs Objects
`print(<glow_pi_case_data>)`	Print Method for glow_pi_case_data
`print(<glow_pi_control_data>)`	Print Method for glow_pi_control_data
`print(<glow_test_result>)`	Print Method for GLOW Test Results
`print(<glow_training_data>)`	Print Method for glow_training_data
`print(<glow_variant_filter>)`	Print Method for Variant Filter Specifications
`save_B_model()`	Save a Trained B Estimation Model
`save_PI_models()`	Save PI Models to Directory
`select_best_model()`	Select Best Regression Model for B Estimation
`select_highlight_regions()`	Select Regions to Highlight on a Manhattan Plot
`standardize_column_names()`	Standardize Column Names in GWAS Data
`summarize_PI_coefficients()`	Summarize PI Model Coefficients
`summary(<glow_outliers>)`	Summary Method for glow_outliers Objects
`summary(<glow_pi_case_data>)`	Summary Method for glow_pi_case_data
`summary(<glow_pi_control_data>)`	Summary Method for glow_pi_control_data
`summary(<glow_training_data>)`	Summary Method for glow_training_data
`train_B_model()`	Train a B Estimation Model from Training Data
`train_PI_models()`	Train PI Ensemble Models
`validate_B_training_data()`	Validate GWAS Data for B Estimation
`validate_correlation_matrix()`	Validate correlation matrix
`validate_genotype_matrix()`	Validate genotype matrix for GLOW tests
`variant_filter()`	Create a Variant Filter Specification

Reference

All functions