# Integrated Exposure-Omics Analysis Powered by Tidy Principles

## Documentation for package ‘tidyexposomics’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

build_ont_annot_app | Build the Ontology Annotation Shiny app
create_exposomicset | Create an Exposomicset Object
download_dataset | Download and cache a tidyexposomics dataset
extract_omics_exposure_df | Extract Merged Omics and Exposure Data Frame
extract_results | Extract Results from 'MultiAssayExperiment' Metadata
extract_results_excel | Export tidyexposomics Results to Excel
extract_top_factor_features | Extract Top Contributing Features for Factors
filter_missing | Filter Features and Variables with High Missingness
filter_non_normal | Filter Non-Normal Exposure Variables
filter_omics | Filter low-quality features in omics assays
filter_sample_outliers | Filter Sample Outliers
load_annotation_data | Load Ontology Data
make_example_data | Generate Example Data for Testing
pivot_exp | Pivot a selected omics dataset from a MultiAssayExperiment into tidybulk format
pivot_feature | Extract Feature Metadata from a MultiAssayExperiment
pivot_sample | Extract Sample Metadata from MultiAssayExperiment or SummarizedExperiment
plot_association | Plot Association Results (Unified Forest Plot)
plot_circos_correlation | Plot Circular Network of Exposure Relationships
plot_correlation_summary | Plot Correlation Summary from Exposure-Feature Correlations
plot_correlation_tile | Plot Correlation Tilemap
plot_enrichment | Plot Enrichment Results from exposomicset
plot_exposures | Plot Exposure Distributions by Category or Group
plot_exposure_impact | Plot Exposure Impact on Network Centrality Metrics
plot_exposure_omics_association | Plot Exposure-Omics Associations
plot_factor_summary | Plot Summary of Factor Contributions from Multi-Omics Integration
plot_manhattan | Plot a Manhattan-style ExWAS summary across omics categories
plot_missing | Plot Missing Data Across Exposure and Omic Layers
plot_network | Plot Network Graph of Features or Exposures
plot_normality_summary | Plot Normality Summary of Exposure Variables
plot_pca | Plot PCA Results for Features and Samples
plot_sample_clusters | Plot Sample Clusters
plot_sensitivity_summary | Plot Sensitivity Analysis Summary
plot_top_factor_features | Plot Top Features by Factor from Integration Results
plot_volcano | Volcano Plot of Differential Abundance
run_association | Run Association Analysis
run_cluster_samples | Cluster Samples Based on Exposure Data
run_correlation | Run Correlation Analysis
run_create_network | Create Correlation Network from Feature Data
run_differential_abundance | Run Differential Abundance Analysis
run_enrichment | Perform enrichment analysis on selected features from a exposomicset object
run_exposome_score | Compute Composite Exposome Scores
run_exposure_impact | Calculate Exposure Impact from Feature-Exposure Correlation Networks
run_exposure_omics_association | Run Exposure-Omics Association
run_factor_overlap | Identify and Annotate Shared Top Features Across Integration Factors
run_impute_missing | Impute Missing Exposure and Omics Data in a MultiAssayExperiment
run_multiomics_integration | Run Multi-Omics Integration
run_normality_check | Assess Normality of Exposure Variables
run_pca | Perform Principal Component Analysis (PCA)
run_pipeline_summary | Summarize and Visualize Analysis Pipeline Steps
run_sensitivity_analysis | Run Sensitivity Analysis for Differential Abundance
run_summarize_exposures | Summarize Exposure Variables
tidyexposomics_example | Example exposome multi-omics dataset
transform_exposure | Transform Exposure Variables for Normality