R/biomarkers.R

In flevr: Flexible, Ensemble-Based Variable Selection with Potentially Missing Data

#' Example biomarker data
#'
#' A dataset inspired by data collected by the Early Detection Research
#' Network (EDRN). Biomarkers developed at six "labs" are validated at
#' at least one of four "validation sites" on 306 cysts. The data also include two binary outcome variables: whether or not the cyst was classified as mucinous,
#' and whether or not the cyst was determined to have high malignant potential.
#'
#' @format `biomarkers`: a tibble with 306 rows and 24 columns, where the first
#'  column is the validation site, the next two columns are the possible outcomes,
#' and the remaining columns are the biomarkers:
#' \describe{
#'   \item{institution}{the validation site}
#'   \item{mucinous}{a binary indicator of whether the cyst was classified as mucinous}
#'   \item{high_malignancy}{a binary indicator of whether the cyst was classified as having high malignant potential}
#'   \item{lab1_actb}{a biomarker}
#'   \item{lab1_molecules_score}{a biomarker}
#'   \item{lab1_telomerase_score}{a biomarker}
#'   \item{lab2_fluorescence_score}{a biomarker}
#'   \item{lab3_muc3ac_score}{a biomarker}
#'   \item{lab3_muc5ac_score}{a biomarker}
#'   \item{lab4_areg_score}{a biomarker}
#'   \item{lab4_glucose_score}{a biomarker}
#'   \item{lab5_mucinous_call}{a biomarker (binary)}
#'   \item{lab5_neoplasia_v1_call}{a biomarker (binary)}
#'   \item{lab5_neoplasia_v2_call}{a biomarker (binary)}
#'   \item{lab6_ab_score}{a biomarker}
#'   \item{cea}{a biomarker}
#'   \item{lab1_molecules_neoplasia_call}{binary indicator of whether \code{lab1_molecules_score} > 25}
#'   \item{lab1_telomerase_neoplasia_call}{binary indicator of whether \code{lab1_telomerase_score} > 730}
#'   \item{lab2_fluorescence_mucinous_call}{binary indicator of whether \code{lab2_fluorescence_score} > 1.23}
#'   \item{lab4_areg_mucinous_call}{binary indicator of whether \code{lab4_areg_score} > 112}
#'   \item{lab4_glucose_mucinous_call}{binary indicator of whether \code{lab4_glucose_score} < 50}
#'   \item{lab4_combined_mucinous_call}{binary indicator of whether \code{lab4_areg_score} > 112 and \code{lab4_glucose_score} < 50}
#'   \item{lab6_ab_neoplasia_call}{binary indicator of whether \code{lab6_ab_score} > 0.104}
#'   \item{cea_call}{binary indicator of whether \code{cea} > 192}
#' }
#' @source Inspired by data collected by the EDRN \url{https://edrn.nci.nih.gov/}.
"biomarkers"