R/example-data.R

In samWieczorek/DAPAR2: Tools for the Differential Analysis of Proteins Abundance with R

#' @title Creates an example dataset
#'
#' @description
#' This function builds a dataset which is an instance of
#' the class [QFeatures].
#'
#' @param with.na A `logical(1)` which indicates whether the
#' example dataset contains missing values or not. Default is FALSE.
#'
#' @return An instance of class [QFeatures]
#'
#' @author Samuel Wieczorek
#'
#' @export
#'
#' @rdname create-example
#'
#' @examples
#' create_ft_example()
#' create_ft_example(TRUE)
#'
#' @importFrom utils read.table
#'
create_ft_example <- function(with.na = FALSE) {
    filename <- if (with.na) "ft-data-na.txt" else "ft-data.txt"
    data.file <- system.file("extdata", filename, package = "DaparToolshed")
    data <- read.table(data.file,
        header = TRUE,
        sep = "\t",
        as.is = TRUE,
        stringsAsFactors = FALSE
    )

    sample.file <- system.file("extdata",
        "ft-samples.txt",
        package = "DaparToolshed"
    )
    sample <- read.table(sample.file,
        header = TRUE,
        sep = "\t",
        as.is = TRUE,
        stringsAsFactors = FALSE
    )

    tmp.qf <- createQFeatures(
      data = data,
      sample = sample,
      indQData = 2:7,
      keyId = "ID",
      analysis = "test",
      indexForMetacell = 9:14,
      typeDataset = "peptide",
      parentProtId = "Proteins",
      force.na = TRUE,
      software = "maxquant"
      )


    if (with.na) {
        ft_na <- tmp.qf
        save(ft_na, file = paste0("data/ft_na.rda"))
        saveRDS(ft_na, file = paste0("inst/extdata/ft_na.qf"))
    } else {
        ft <- tmp.qf
        save(ft, file = paste0("data/ft.rda"))
        saveRDS(ft, file = paste0("inst/extdata/ft.qf"))
    }

    tmp.qf
}