@@ -27,7 +27,9 @@ Suggests:

     Rtsne,

     vsn,

     VIM,

-    pcaMethods

+    pcaMethods,

+    testthat (>= 3.0.0)

 Depends: 

     R (>= 2.10),

     SummarizedExperiment

+Config/testthat/edition: 3

deleted file mode 100644

@@ -1,48 +0,0 @@

-##' @export

-pqn_args <- function(dat_in, dat_out, ref_ids = NULL, min_frac = 0.5,

-                     type = "mean") {

-  new("pqn_args", dat_in = dat_in, dat_out = dat_out,

-      ref_ids = ref_ids, min_frac = min_frac)

-}

-

-sample_normalizer_args <- function(...) {

-  new("sample_normalizer_args", ...)

-}

-

-sum_args <- function(dat_in, dat_out, restrict = TRUE, rescale = FALSE) {

-  new("sample_normalizer_args", normalizer = "sum",

-      dat_in = dat_in, dat_out = dat_out,

-      restrict = restrict, rescale = rescale)

-}

-

-mean_args <- function(dat_in, dat_out, restrict = TRUE, rescale = FALSE) {

-  new("sample_normalizer_args", normalizer = "mean",

-      dat_in = dat_in, dat_out = dat_out,

-      restrict = restrict, rescale = rescale)

-}

-

-median_args <- function(dat_in, dat_out, restrict = TRUE, rescale = FALSE) {

-  new("sample_normalizer_args", normalizer = "median",

-      dat_in = dat_in, dat_out = dat_out,

-      restrict = restrict, rescale = rescale)

-}

-

-mad_args <- function(dat_in, dat_out, restrict = TRUE, rescale = FALSE) {

-  new("sample_normalizer_args", normalizer = "mad",

-      dat_in = dat_in, dat_out = dat_out,

-      restrict = restrict, rescale = rescale)

-}

-

-euclidean_args <- function(dat_in, dat_out, restrict = TRUE, rescale = FALSE) {

-  new("sample_normalizer_args", normalizer = "euclidean",

-      dat_in = dat_in, dat_out = dat_out,

-      restrict = restrict, rescale = rescale)

-}

-

-cyclicloess_args <- function(dat_in, dat_out, weights = NULL, span = 0.7,

-                             iterations = 3, method = "fast") {

-  new("cyclicloess_args", 

-      dat_in = dat_in, dat_out = dat_out,

-      weights = weights, span = span, iterations = as.integer(iterations),

-      method = method)

-}

deleted file mode 100644

@@ -1,129 +0,0 @@

-## List coercion method

-##' @export

-as.list.poplinArgs <- function(x) {

-  snames <- slotNames(x)

-  internals <- grep(snames, pattern = "^\\.")

-  if (length(internals)) {

-    ## Exclude hidden slots

-    snames <- snames[-internals]

-  }

-  ## args_list <- vector("list", length(snames)) # empty list

-  ## names(args_list) <- snames

-  ## for (i in names(args_list)) {

-  ##   args_list[[i]] <- slot(x, name = i)

-  ## }

-  args_list <- lapply(snames, function(name) slot(x, name))

-  names(args_list) <- snames

-  args_list

-}

-

-setMethod("as.list", "poplinArgs", as.list.poplinArgs)

-

-##' @exportMethod coerce

-setAs("poplinArgs", "list", function(from) {

-  as.list(from)

-})

-

-## Show method

-.poplinArgs_show <- function(object) {

-  cat("Class: ", class(object), "\n", sep = "")

-  cat(" Arguments:\n")

-  poplin_args <- as.list(object)

-  for (i in seq_along(poplin_args)) {

-    cat(" - ", names(poplin_args)[i], ": ", deparse(poplin_args[[i]]), "\n",

-        sep = "")

-  }

-}

-

-setMethod("show", "poplinArgs", .poplinArgs_show)

-

-.slot_check <- function(object) {

-  snames <- slotNames(object)

-  slot_check <- sapply(slotNames(object), function(x) !.hasSlot(object, x))

-  if (sum(slot_check) == 0) {

-    character(0)

-  } else {

-    paste0("Slots not found: ", snames[slot_check])

-  }

-}

-

-.pqn_args_validity <- function(object) {

-  msg <- .slot_check(object)

-  if (length(object@dat_in) != 1) {

-    msg <- c(msg, "'dat_in' must be a character of length 1.")

-  }

-  if (length(object@dat_out) != 1) {

-    msg <- c(msg, "'dat_out' must be a character of length 1.")

-  }

-  if (length(object@min_frac) != 1 || object@min_frac < 0 ||

-      object@min_frac > 1) {

-    msg <- c(msg, "'min_frac' must be a numeric value between 0 and 1.")

-  }

-  if (length(object@type) != 1 || !(object@type %in% c("mean", "median"))) {

-    msg <- c(msg, "'type' must be either \"mean\" or \"median\".")

-  }

-  if (length(msg)) {

-    msg

-  } else TRUE

-}

-

-setValidity("pqn_args", .pqn_args_validity)

-

-.sample_normalizer_args_validity <- function(object) {

-  msg <- .slot_check(object)

-  normalizer_allowed <- c("sum", "mean", "median", "mad", "euclidean")

-  if (length(object@normalizer) != 1 ||

-      !(object@normalizer %in% normalizer_allowed)) {

-    msg <- c(

-      msg,

-      paste0("'normalizer' must be one of ",

-             paste0("'", normalizer_allowed, "'", collapse = ", "), ".")

-    )

-  }

-  if (length(object@dat_in) != 1) {

-    msg <- c(msg, "'dat_in' must be a character of length 1.")

-  }

-  if (length(object@dat_out) != 1) {

-    msg <- c(msg, "'dat_out' must be a character of length 1.")

-  }

-  if (length(object@restrict) != 1) {

-    msg <- c(msg, "'restrict' must be a logical of length 1.")

-  }

-  if (length(object@rescale) != 1) {

-    msg <- c(msg, "'rescale' must be a logical of length 1.")

-  }

-  if (length(msg)) {

-    msg

-  } else TRUE

-}

-

-setValidity("sample_normalizer_args", .sample_normalizer_args_validity)

-

-.cyclicloess_args_validity <- function(object) {

-  msg <- .slot_check(object)

-  ## if (length(object@normalizer) != 1 || object@normalizer != "cyclicloess") {

-  ##   msg <- c(msg, "'normalizer' must be cyclicloess.")

-  ## }

-  if (length(object@dat_in) != 1) {

-    msg <- c(msg, "'dat_in' must be a character of length 1.")

-  }

-  if (length(object@dat_out) != 1) {

-    msg <- c(msg, "'dat_out' must be a character of length 1.")

-  }

-  if (length(object@span) != 1 || object@span < 0 || object@span > 1) {

-    msg <- c(msg, "'span' must be a numeric value between 0 and 1.")

-  }

-  if (length(object@iterations) != 1 || object@iterations <= 0) {

-    msg <- c(msg, "'iterations' must be a positive integer.")

-  }

-  method_allowed <- c("pairs", "fast", "affy")

-  if (length(object@method) != 1 || !(object@method %in% method_allowed)) {

-    msg <- c(

-      msg,

-      paste0("'method' must be one of ",

-             paste0("'", method_allowed, "'", collapse = ", "), ".")

-    )

-  }

-}

-

-setValidity("cyclicloess_args", .cyclicloess_args_validity)