extr_tetramer: 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,
  ...
)

Value

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

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.

References

Comparative Toxicogenomics Database: https://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. 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. tools:::Rd_expr_doi("10.1093/toxsci/kfad069")

Examples

Run this code

# \donttest{
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)
# }