data-raw/DATASET.R

In compbiomed/curatedTBData: Curation of existing tuberculosis transcriptomic studies

## code to prepare `DATASET` dataset goes here

# usethis::use_data("DATASET")
# usethis::use_data(NameOfTheDataset, compress = "xz", overwrite = TRUE)
library(purrr)
library(devtools)
# dataNamesAll <- list.files("data-raw/", pattern = "*.RDS")
# dataPathFull <- list.files("data-raw", pattern = "*.RDS", full.names = TRUE)
# dataAllList <- lapply(dataPathFull, function(x) readRDS(x))
# names(dataAllList) <- gsub("\\..*", "", dataNamesAll)
# purrr::walk2(dataAllList, paste0(names(dataAllList)), function(obj, name) {
#   assign(name, obj)
#   do.call("use_data", list(as.name(name), compress = "xz", overwrite = TRUE))
# })

# Save summary table
DataSummary_raw <- readxl::read_excel("data-raw/Data_summaryforpackage.xlsx",
                                  sheet = "DataSummary")
DataSummary <- DataSummary_raw[-base::nrow(DataSummary_raw),] |>  ## Remove the last row: Total
  base::as.data.frame()
usethis::use_data(DataSummary, compress = "xz", overwrite = TRUE)

# Save training table
SignatureInfoTraining_raw <- readxl::read_excel("data-raw/Data_summaryforpackage.xlsx",
                                            sheet = "SignatureInfoTraining")
SignatureInfoTraining <- SignatureInfoTraining_raw %>%
  dplyr::filter(.data$Study != "Unable to find training data") %>% ## Remove signatures with unidentified discovery datasets
  base::as.data.frame()
usethis::use_data(SignatureInfoTraining, compress = "xz", overwrite = TRUE)

# Save clinical information table
Clinical_Information <- readxl::read_excel("data-raw/Data_summaryforpackage.xlsx",
                                                sheet = "Clinical_Information")
usethis::use_data(Clinical_Information, compress = "xz", overwrite = TRUE)