extr_tetramer: Extract Tetramer Data from the CTD API

In extractox: Extract Tox Info from Various Databases

Extract Tetramer Data from the CTD API

Description

This function queries the Comparative Toxicogenomics Database API to retrieve tetramer data based on chemicals, diseases, genes, or other categories.

Usage

extr_tetramer(
  chem,
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals",
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)

Arguments

chem	A string indicating the chemical identifiers such as CAS number or IUPAC name of the chemical.
disease	A string indicating a disease term. Default is an empty string.
gene	A string indicating a gene symbol. Default is an empty string.
go	A string indicating a Gene Ontology term. Default is an empty string.
input_term_search_type	A string specifying the search method to use. Options are "hierarchicalAssociations" or "directAssociations". Default is "directAssociations".
qt_match_type	A string specifying the query type match method. Options are "equals" or "contains". Default is "equals".
verify_ssl	Boolean to control if SSL should be verified or not. Default is FALSE.
verbose	A logical value indicating whether to print detailed messages. Default is TRUE.
...	Any other arguments to be supplied to req_option and thus to libcurl.

Value

A data frame containing the queried tetramer data in CSV format.

References

• Comparative Toxicogenomics Database: http://ctdbase.org

• Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, T. C., & Mattingly, C. J. (2019). The Comparative Toxicogenomics Database: update 2019. Nucleic acids research, 47(D1), D948–D954. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/nar/gky868")}

• Davis, A. P., Wiegers, T. C., Wiegers, J., Wyatt, B., Johnson, R. J., Sciaky, D., Barkalow, F., Strong, M., Planchart, A., & Mattingly, C. J. (2023). CTD tetramers: A new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health. Toxicological Sciences, 195(2), 155–168. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/toxsci/kfad069")}

See Also

Comparative Toxicogenomics Database

Examples

tetramer_data <- extr_tetramer(
  chem = c("50-00-0", "ethanol"),
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals"
)
str(tetramer_data)

extractox documentation built on April 4, 2025, 2:30 a.m.