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ctdR: Enrichment Analysis of Chemical-Gene Interactions from CTD

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

ctdR identifies chemicals significantly associated with a set of genes using data from the Comparative Toxicogenomics Database (CTD, https://ctdbase.org).

Four enrichment methods are supported through a unified interface:

ORA

Over-Representation Analysis via phyper.

GSEA

Gene Set Enrichment Analysis via fgsea.

CAMERA

Competitive gene-set test accounting for inter-gene correlation, via camera.

GSVA

Per-sample Gene Set Variation Analysis via gsva.

ORA and GSEA take a gene-level data frame. CAMERA and GSVA take expression data, either as a numeric matrix (genes x samples) or as a SummarizedExperiment; GSVA returns its per-sample scores in whichever of the two it was given, so sample annotation stays attached to the results.

Quick Start

  1. Download CTD_chem_gene_ixns.csv.gz from https://ctdbase.org/reports/CTD_chem_gene_ixns.csv.gz and decompress it (gunzip CTD_chem_gene_ixns.csv.gz).

  2. Import the data once: import_CTD("path/to/CTD_chem_gene_ixns.csv")

  3. Run enrichment analysis: enrichment_CTD(my_genes, method = "ORA")

Data Licensing Disclaimer

This package does not bundle, redistribute, or embed any data from the Comparative Toxicogenomics Database. CTD data are created and maintained by NC State University and are subject to specific licensing terms and conditions.

Users are solely responsible for:

  • Downloading the required data files directly from https://ctdbase.org.

  • Reading and accepting the CTD Terms of Service at https://ctdbase.org/about/legal.jsp before using the data.

  • Complying with all applicable CTD data licensing requirements, including proper citation of CTD in any publications or derived works.

By using ctdR with CTD data, you acknowledge that you have read, understood, and agreed to the CTD Terms of Service.

References

Davis AP, Wiegers TC, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ (2023). "Comparative Toxicogenomics Database (CTD): update 2023." Nucleic Acids Research, 51(D1), D1257-D1262. doi:10.1093/nar/gkac833 . https://ctdbase.org

See also

import_CTD to import CTD data, enrichment_CTD to run enrichment analysis.

Author

Maintainer: Luigi Corsaro lcorsaro69@gmail.com (ORCID)

Authors: