delete accessors

Author: FeiLiyang

R/helpers.R

@@ -62,89 +62,6 @@ returnNumMat <- function(object) {
     return(objectUpdated)
 }
 
-#' Check if `barbieQ` object is in right format
-#'
-#' `checkBarbieQDimensions()` ensures that the `proportion`, `CPM`, `occurrence`,
-#'  and `rank` components of `barbieQ` have the same number of samples and
-#'  Barcodes as `assay`.
-#'
-#' @param barbieQ A `barbieQ` object created by the [createBarbieQ] function.
-#'
-#' @return a logical value
-#'  * Returns TRUE if components in the `barbieQ` object are correctly formatted.
-#'  * Otherwise, the function throws an error with specific a reason.
-#'
-#' @noRd
-#'
-#' @examples \donttest{
-#' Treat <- factor(rep(seq_len(2), each = 6))
-#' Time <- rep(rep(seq_len(2), each = 3), 2)
-#' nbarcodes <- 50
-#' nsamples <- 12
-#' count <- abs(matrix(rnorm(nbarcodes * nsamples), nbarcodes, nsamples))
-#' rownames(count) <- paste0('Barcode', seq_len(nbarcodes))
-#' barbieQ <- createBarbieQ(count, data.frame(Treat = Treat, Time = Time))
-#' barbieQ:::checkBarbieQDimensions(barbieQ)
-#' }
-checkBarbieQDimensions <- function(barbieQ) {
-    ## check barbieQ$assay's format
-    if (is.data.frame(barbieQ$assay) || is.matrix(barbieQ$assay)) {
-        NumDim <- dim(barbieQ$assay)
-    } else {
-        stop("barbieQ$assay wrong format.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-    }
-    ## check barbieQ$metadata's format and dimension
-    if (is.data.frame(barbieQ$metadata) || is.matrix(barbieQ$metadata)) {
-        if (nrow(barbieQ$metadata) != NumDim[2]) {
-            stop("row dimension of barbieQ$metadata doesn't match column dimention of barbieQ$assay.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-        }
-    } else {
-        stop("BarbieQ$assay wrong format.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-    }
-    ## check other components' format dimensions
-    elements <- c("proportion", "CPM", "occurrence", "rank")
-    for (elem in elements) {
-        if (is.data.frame(barbieQ[[elem]]) || is.matrix(barbieQ[[elem]])) {
-            elemDim <- dim(barbieQ[[elem]])
-            if (any(elemDim != NumDim)) {
-                stop("dimensions of barbieQ component-", elem, "don't match dimentions of barbieQ$assay.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-            }
-        } else {
-            stop("barbieQ component-", elem, " isn't in right format.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-        }
-    }
-    ## check barbieQ$isTop format and dimensions
-    if (!is.null(barbieQ$isTop$vec)) {
-        if (is.vector(barbieQ$isTop$vec)) {
-            if (length(barbieQ$isTop$vec) != NumDim[1]) {
-                stop("length of barbieQ$isTop$vec doesn't match row dimention of barbieQ$assay.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-            }
-        } else {
-            stop("BarbieQ$isTop$vec isn't in right format.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-        }
-    }
-    if (!is.null(barbieQ$isTop$mat)) {
-        if (is.matrix(barbieQ$isTop$mat) || is.data.frame(barbieQ$isTop$mat)) {
-            if (nrow(barbieQ$isTop$mat) != NumDim[1]) {
-                stop("row dimension barbieQ$isTop$mat doesn't match row dimention of barbieQ$assay.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand.")
-            }
-        } else {
-            stop("barbieQ$isTop$mat isn't in right format.
-call createBarbieQ() to generate proper `barbieQ` object - don't modify by hand..")
-        }
-    }
-
-    return(TRUE)
-}
-
 #' Extract sampleMetadata and primary factor
 #'
 #' `extractSampleMetadataAndPrimaryFactor()` extracts sampleMetadata `data.frame` from the