extr_tetramer {extractox} | R Documentation |
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 |
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
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)