move limma to suggestions

Author: person-c

DESCRIPTION

@@ -25,6 +25,7 @@ Suggests:
     rmarkdown,
     ggrepel,
     Seurat,
+    limma,
     GEOquery,
     fgsea,
     edgeR,

NAMESPACE

@@ -41,5 +41,4 @@ import(graphics)
 import(stats)
 import(utils)
 importFrom(data.table,data.table)
-importFrom(limma,makeContrasts)
 importFrom(utils,download.file)

R/limma.R

@@ -83,6 +83,10 @@ dprocess_dgeList <- function(x, group.column, min.count = 10) {
   lcpm <- edgeR::cpm(x, log = TRUE)
   boxplot(lcpm, las = 2)
   title("Normalized data")
+
+  if (requireNamespace("limma", quietly = TRUE)) {
+    stop("To plot MDS plot, 'plotMDS' requires 'limma' package which cannot be found. Please install 'limma' using 'BiocManager::install('limma')'")
+  }
   limma::plotMDS(lcpm,
     label = x$samples[[group.column]],
     col = as.integer((x$samples[[group.column]])), dim = c(1, 2)
@@ -106,14 +110,13 @@ dprocess_dgeList <- function(x, group.column, min.count = 10) {
 #' @return An `eBayes` object containing the fitted linear model and
 #'   results of the differential expression analysis.
 #' @import data.table
-#' @importFrom limma makeContrasts
 #' @export
 limmaFit <- function(x, group.column) {
   oldpar <- par(no.readonly = TRUE)
   on.exit(par(oldpar))
 
   if (!requireNamespace("limma", quietly = TRUE)) {
-    stop("To fit linear model, limmaFit) requires 'limma' package which cannot be found. Please install 'limma' using 'BiocManager::install('limma')'.")
+    stop("To fit linear model, 'limmaFit' requires 'limma' package which cannot be found. Please install 'limma' using 'BiocManager::install('limma')'.")
   }
   makeContrasts <- limma::makeContrasts()