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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,
  ...
)

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.

...

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"
)
#> Sending request to CTD database for tetramer data for 50-00-0...
#> Request succeeded with status code: 200
#> Sending request to CTD database for tetramer data for ethanol...
#> Request succeeded with status code: 200
str(tetramer_data)
#> 'data.frame':	50073 obs. of  9 variables:
#>  $ query       : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
#>  $ chemical    : chr  "Formaldehyde" "Formaldehyde" "Formaldehyde" "Formaldehyde" ...
#>  $ chemical_id : chr  "D005557" "D005557" "D005557" "D005557" ...
#>  $ gene        : chr  "PTEN" "PTEN" "NLGN4X" "PTEN" ...
#>  $ gene_id     : int  5728 5728 57502 5728 5728 7846 1813 23657 5728 1813 ...
#>  $ phenotype   : chr  "adult behavior" "adult behavior" "adult behavior" "adult behavior" ...
#>  $ phenotype_id: chr  "GO:0030534" "GO:0030534" "GO:0030534" "GO:0030534" ...
#>  $ disease     : chr  "Adenocarcinoma" "Asthma" "Autistic Disorder" "Autistic Disorder" ...
#>  $ disease_id  : chr  "D000230" "D001249" "D001321" "D001321" ...
# }