Package index • tidyexposomics

Correlation/Association

Run Pipelines

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 expomicset object

run_exposome_score(): Compute Composite Exposome Scores

run_exposure_impact(): Calculate Exposure Impact from Feature-Exposure Correlation Networks

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

Data Processing

create_expomicset(): Create an expomicset Object

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

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

transform_exposure(): Transform Exposure Variables for Normality

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

Data Visualization

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 ExpOmicSet

plot_exposures(): Plot Exposure Distributions by Category or Group

plot_exposure_impact(): Plot Exposure Impact on Network Centrality Metrics

plot_factor_summary(): Plot Summary of Factor Contributions from Multi-Omics Integration

plot_heatmap_correlate_exposure(): Correlation Heatmap of Exposure Variables with Category Annotations

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

Ontology Annotation App

ont_annot_app(): Launch Ontology Annotation Shiny App

Example Data

chebi: ChEBI Ontology Table (Chemical Entities of Biological Interest)

hpo: HPO Ontology Table (Human Phenotype Ontology)

ecto: ECTO Ontology Table (Environmental Conditions, Treatments & Exposures)

annotated_cb: Annotated Exposure Codebook (ISGlobal Exposome Challenge)

meta: Sample-Level Metadata for the Exposome Challenge Dataset

fdata: Feature Metadata for Multi-Omics Assays

omics_list: Multi-Omics Assays for the Exposome Dataset