data-raw/DATASET.R

In openpharma/visR: Clinical Graphs and Tables Adhering to Graphical Principles

## code to prepare `DATASET` dataset goes here

usethis::use_data("DATASET")

# Breast survival data

library(dplyr)
library(RTCGA)
library(RTCGA.clinical)

brca_cohort <- survivalTCGA(
  BRCA.clinical,
  extract.cols = c(
    "admin.disease_code",
    "patient.breast_carcinoma_estrogen_receptor_status",
    "patient.breast_carcinoma_progesterone_receptor_status",
    "patient.clinical_cqcf.tumor_type",
    "patient.drugs.drug.therapy_types.therapy_type",
    "patient.age_at_initial_pathologic_diagnosis"
  )
) %>%
  dplyr::rename(
    tumor_type = patient.clinical_cqcf.tumor_type,
    therapy = patient.drugs.drug.therapy_types.therapy_type,
    er_status = patient.breast_carcinoma_estrogen_receptor_status,
    progesterone_status = patient.breast_carcinoma_progesterone_receptor_status,
    dx_age = patient.age_at_initial_pathologic_diagnosis,
    followup_time = times
  ) %>%
  dplyr::mutate(
    er_status = factor(er_status),
    progesterone_status = factor(progesterone_status),
    dx_age = as.numeric(dx_age),
    dx_age_group = factor(
      case_when(
        dx_age < 30 ~ "< 30y",
        dx_age >= 30 &
          dx_age <= 50 ~ "30-50y",
        dx_age > 50 &
          dx_age <= 70 ~ "51-70y",
        dx_age > 70 ~ "> 70y"
      ),
      levels = c("< 30y", "30-50y", "51-70y", "> 70y")
    )
  )

usethis::use_data(brca_cohort)