Skip to contents

Extract Tetramer Data from the CTD API

Source: R/extr_ctd.R
extr_tetramer.Rd

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. 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. doi:10.1093/toxsci/kfad069

See also

Comparative Toxicogenomics Database

Examples

# \donttest{
tetramer_data <- extr_tetramer(
  chem = c("50-00-0", "ethanol"),
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals"
)
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> ℹ Sending request to CTD database for tetramer data for
#> 50-00-0...
#> ℹ Request succeeded with status code: 200
#> ℹ Sending request to CTD database for tetramer data for
#> ethanol...
#> ℹ Request succeeded with status code: 200
str(tetramer_data)
#> 'data.frame':	50421 obs. of  10 variables:
#>  $ chemical               : chr  "Formaldehyde" "Formaldehyde" "Formaldehyde" "Formaldehyde" ...
#>  $ chemical_id            : chr  "D005557" "D005557" "D005557" "D005557" ...
#>  $ gene                   : chr  "IL1B" "IL1B" "IFNG" "IL6" ...
#>  $ gene_id                : int  3553 3553 3458 3569 3569 3569 7124 7124 7124 7124 ...
#>  $ phenotype              : chr  "apoptotic process" "apoptotic process" "apoptotic process" "inflammatory response" ...
#>  $ phenotype_id           : chr  "GO:0006915" "GO:0006915" "GO:0006915" "GO:0006954" ...
#>  $ disease                : chr  "Inflammation" "Hyperalgesia" "Dermatitis, Allergic Contact" "Inflammation" ...
#>  $ disease_id             : chr  "D007249" "D006930" "D017449" "D007249" ...
#>  $ evidence_strength_score: int  4860 4320 3900 2376 2376 2376 2016 2016 2016 2016 ...
#>  $ query                  : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
# }