R/data.R

In pwatrick/DrugRepurposingToolKit: A High-Throughput Approach Integrating Gene Expression Signatures and Clinical Data to Repurpose Drugs

#' @importFrom tibble tibble
NULL

#' ohdsi_icd_elix
#'
#' For extracting ICD codes from OMOP CDM to calculate Elixhauser comorbidity scores
#'
#' @format A data frame with 5 variables: \code{concept_id}, \code{concept_name}, \code{vocabulary_id}, \code{concept_code}, \code{concept_code_strip}
#' @source Elixhauser, A., Steiner, C., Harris, D. R. & Coffey, R. M. Comorbidity measures for use with administrative data. Med. Care 36, 8–27 (1998)
#' @source van Walraven C, Austin PC, Jennings A, Quan H and Forster AJ. A modification of the Elixhauser comorbidity measures into a point system for hospital death using administrative data. Medical Care 2009; 47(6):626-633. DOI: 10.1097/MLR.0b013e31819432e5
"ohdsi_icd_elix"

#' vw_weights
#'
#' For calculating Elixhauser comorbidity scores
#'
#' @format A data frame with 2 variables: \code{group} and \code{weight}
#' @format A data frame with 31 rows and 2 variables:
#' \describe{
#'   \item{group}{Elixhauser comorbidity group. From Elixhauser et al 1998}
#'   \item{weight}{Comorbidity weight. From van Walraven et al 2009}
#' }
#' @source Elixhauser, A., Steiner, C., Harris, D. R. & Coffey, R. M. Comorbidity measures for use with administrative data. Med. Care 36, 8–27 (1998)
#' @source van Walraven C, Austin PC, Jennings A, Quan H and Forster AJ. A modification of the Elixhauser comorbidity measures into a point system for hospital death using administrative data. Medical Care 2009; 47(6):626-633. DOI: 10.1097/MLR.0b013e31819432e5
"vw_weights"

#' dr_ts_tutorial_data
#'
#'
#' @format List with five objects:
#'          c("spredixcan_phenotype_ts", "cmap_genes",
#'          "ilincs_output", "ilincs_simvastatin_dm4740", "pres_drugs")
"dr_ts_tutorial_data"

#' drugsHyperlipidemia
#'
#' Known lipid-lowering drugs
#'
#' @format A data frame with 3 variables: \code{rxcui_in}, \code{drug_desc} and
#'   \code{indication}
#' @format A data frame with 134 rows and 3 variables:
#' \describe{
#'   \item{rxcui_in}{RxCUI ingredients}
#'   \item{drug_desc}{Name of active drug ingredient}
#'   \item{indication}{Drug indication}
#'   ...
#' }
#' @source MEDI-HPS (Wei W-Q, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC.
#'         2013. Development and evaluation of an ensemble resource linking
#'         medications to their indications. J Am Med Inform Assoc 20:954–961.)
"drugsHyperlipidemia"

#' drugsHypertension
#'
#' Known antihypertensive drugs
#'
#' @format A data frame with 3 variables: \code{rxcui_in}, \code{drug_desc} and
#'   \code{indication}
#' @format A data frame with 134 rows and 3 variables:
#' \describe{
#'   \item{rxcui_in}{RxCUI ingredients}
#'   \item{drug_desc}{Name of active drug ingredient}
#'   \item{indication}{Drug indication}
#'   ...
#' }
#' @source MEDI-HPS (Wei W-Q, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC.
#'         2013. Development and evaluation of an ensemble resource linking
#'         medications to their indications. J Am Med Inform Assoc 20:954–961.)
"drugsHypertension"

#' ddi_rxcui2in
#'
#' Map rxcuis to their rxcui ingredients
#'
#' @format A data frame with 3 variables: \code{rxcui_ingr}, \code{rxcui} and
#'   \code{rxcui_ingr_name}
"ddi_rxcui2in"

#' ddi_rxcui_names
#'
#' Map rxcuis to their names
#'
#' @format A data frame with 3 variables: \code{drug_name}, \code{vocabulary_id} and
#'   \code{rxcui}
"ddi_rxcui_names"

#' ddi_ohdsi_rxnorm
#'
#' Map rxcuis to their names
#'
#' @format A data frame with 2 variables: \code{concept_id}, \code{rxcui}
"ddi_ohdsi_rxnorm"