R/checks.r

In mimager: mimager: The Microarray Imager

check_trim <- function(x) {
  if (length(x) == 1) {
    if (x >= 0 && x <= 1) return(x)
  } else if (length(x) == 2) {
    return(x)
  }
  stop("trim must be either a single value between 0 and 1 or a vector of ",
       "2 values defining a range.",
       call. = FALSE)
}

check_type <- function(object, type) {
  if (is.null(type)) type <- "pm"
  choices <- switch(class(object),
    AffyBatch            = c("all", "pm", "mm"),
    ExpressionFeatureSet = c("all", "pm", "mm"),
    GeneFeatureSet       = c("all", "pm", "bg"),
    ExonFeatureSet       = c("all", "pm", "mm", "bg"),
    SnpFeatureSet        = c("all", "pm", "mm"),
    PLMset               = c("residuals", "weights"),
    oligoPLM             = c("residuals", "weights")
  )
  if (all(type %in% choices)) return(type)
  stop(
    "Invalid type for ", class(object), " should be one of ",
    paste(choices, collapse = ", "),
    call. = FALSE
  )
}

# check for annotation packages
check_annotation <- function(x) {
  stopifnot(is.character(x))
  status <- suppressPackageStartupMessages(
    require(x, character.only = TRUE, quietly = TRUE)
  )
  if (status) return(x)
  stop(
    x, "Please install ", x, " from Biocounductor.\n",
    "BiocManager::install(", x, ")\n",
    call. = FALSE
  )
}