removed set_seed() from DESeq2 negative binomial check

NAMESPACE

@@ -20,7 +20,6 @@ export(dendrogram_plotter)
 export(goodness_of_fit_DESeq2)
 export(heatmap_num_to_char_converter)
 export(heatmap_plotter)
-export(limma_correction)
 export(normalize_SE)
 export(process_dendrogram)
 export(pval_plotter)

R/negative_binomial_check.R

@@ -31,7 +31,6 @@ counts2pvalue <- function(counts, size, mu) {
 #' @param other_variables name of the se colData containing other variables of
 #'   interest that should be considered in the DESeq2 model
 #' @param num_genes downsample value, default is 500 (or all genes if less)
-#' @param seeding integer to set the seed to for reproducibility; default is 13
 #' @return a matrix of pvalues where each row is a gene and each column is a
 #'   level within the condition of interest
 #' @export
@@ -49,9 +48,7 @@ counts2pvalue <- function(counts, size, mu) {
 
 
 goodness_of_fit_DESeq2 <- function(se, count_matrix, condition,
-    other_variables = NULL, num_genes = 500, seeding = 13) {
-    # set seed
-    set.seed(seeding)
+    other_variables = NULL, num_genes = 500) {
     # Obtain needed data from se object
     count_matrix <- SummarizedExperiment::assays(se)[[count_matrix]]
     condition <- SummarizedExperiment::colData(se)[[condition]]

inst/shiny/server/server_01_upload.R

@@ -271,8 +271,7 @@ observeEvent(input$nb_check, {
             input$counts_matrix,
             input$condition_of_interest,
             input$nb_variables,
-            input$num_genes,
-            input$set_seed)
+            input$num_genes)
         output$recommendation <- renderText(check_res$recommendation)
         output$nb_histogram <- renderPlot(check_res$res_histogram)
         output$reference <- renderText(check_res$reference)

inst/shiny/ui/ui_01_upload.R

@@ -174,11 +174,7 @@ tabPanel("Upload Data",
                         numericInput('num_genes',
                             'Number of genes to analyze (downsampling)',
                             value = 500,
-                            min = 2),
-                        numericInput('set_seed',
-                            'Number to set seed to for reproducibility',
-                            value = 13,
-                            min = 0)),
+                            min = 2)),
                     withBusyIndicatorUI(actionButton(inputId = 'nb_check',
                         label = 'Check Distribution')),
                     textOutput('recommendation'),