converter(DIANN): Enable q-value filtering accounting for MBR

Vitek-Lab · Jan 17, 2025 · 22b30dd · 22b30dd
1 parent ef400ad
commit 22b30dd
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/R/module-loadpage-ui.R b/R/module-loadpage-ui.R
@@ -298,6 +298,9 @@ loadpageUI <- function(id) {
                          conditionalPanel(condition = "input['loadpage-filetype'] == 'sky' || input['loadpage-filetype'] == 'spec'|| input['loadpage-filetype'] == 'diann' ",
                                           checkboxInput(ns("q_val"), "Filter with Q-value"),
                                           conditionalPanel(condition = "input['loadpage-q_val']",
+                                                           conditionalPanel(condition = "input['loadpage-filetype'] == 'diann'",
+                                                                            checkboxInput(ns("MBR"), "MBR Enabled", value = FALSE)
+                                                           ),
                                                            numericInput(ns("q_cutoff"), "Q-value cutoff", 0.01, 0, 1, 0.01))),
                          conditionalPanel(condition = "input['loadpage-filetype'] == 'open'",
                                           checkboxInput(ns("m_score"), "Filter with M-score"),

diff --git a/R/utils.R b/R/utils.R
@@ -518,17 +518,20 @@ getData <- function(input) {
       print(input$dianndata$datapath)
 
       qvalue_cutoff = 0.01
+      MBR = FALSE
       if (input$q_val) {
         qvalue_cutoff = input$q_cutoff
+        MBR = input$MBR
       }
 
       mydata = DIANNtoMSstatsFormat(data,
                                     annotation = getAnnot(input),
                                     qvalue_cutoff = qvalue_cutoff,
+                                    MBR = MBR,
                                     removeProtein_with1Feature = TRUE,
                                     removeFewMeasurements = FALSE,
-                                    use_log_file = FALSE,
-                                    MBR = FALSE)
+                                    use_log_file = FALSE
+      )
       print("Mydata from mstats")
       print(mydata)
     }