@@ -24,6 +24,7 @@ initializeGRN <- function(objectMetadata = list(),

   if (!dir.exists(outputFolder)) {

     dir.create(outputFolder)

   }

+  

   # Create an absolute path out of the given outputFolder now that it exists

   outputFolder = tools::file_path_as_absolute(outputFolder)

   checkmate::assertDirectory(outputFolder, access = "w")

@@ -4132,6 +4133,13 @@ getGRNConnections <- function(GRN, type = "all.filtered",  permuted = FALSE, inc

     }

   } else {

+    # TODO: Re-create the output folder here nd adjust to the OS-specific path separator, do not rely on what is stored in the object

+    if (.Platform$OS.type == "windows") {

+      GRN@config$directories$output_plots = gsub('/', ('\\'), GRN@config$directories$output_plots, fixed = TRUE)

+    } else {

+      GRN@config$directories$output_plots = gsub("\\", "/", GRN@config$directories$output_plots, fixed = TRUE)

+    }

+    

     if (!dir.exists(GRN@config$directories$output_plots)) {

       dir.create(GRN@config$directories$output_plots, recursive = TRUE)

     }

@@ -4371,8 +4379,8 @@ getBasic_metadata_visualization <- function(GRN, forceRerun = FALSE) {

 changeOutputDirectory <- function(GRN, outputDirectory = ".") {

   GRN@config$directories$outputRoot   =  outputDirectory

-  GRN@config$directories$output_plots = paste0(outputDirectory, "/plots/")

-  GRN@config$files$output_log         = paste0(outputDirectory, "GRN.log")

+  GRN@config$directories$output_plots = paste0(outputDirectory, .Platform$file.sep, "plots", .Platform$file.sep)

+  GRN@config$files$output_log         = paste0(outputDirectory, .Platform$file.sep, "GRN.log")

   futile.logger::flog.info(paste0("Output directory changed in the object to " , outputDirectory))