fix(diann): Add q-value filtering to DIANN big clean function (#11)

Author: tonywu1999

.github/.DS_Store

@@ -0,0 +1,18 @@
+# Motivation and Context
+
+Please include relevant motivation and context of the problem along with a short summary of the solution.
+
+## Changes
+
+Please provide a detailed bullet point list of your changes.
+
+- 
+
+## Testing
+
+Please describe any unit tests you added or modified to verify your changes.
+
+## Checklist Before Requesting a Review
+- [ ] I have read the MSstats [contributing guidelines](https://github.com/Vitek-Lab/MSstatsConvert/blob/master/.github/CONTRIBUTING.md)
+- [ ] My changes generate no new warnings
+- [ ] Any dependent changes have been merged and published in downstream modules

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+name: Dry runs for PRs
+on: 
+  pull_request:
+    branches: [devel]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: devel
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Build, Install, Check
+        uses: grimbough/bioc-actions/build-install-check@v1
+

.github/workflows/dry-run-build.yml

@@ -49,10 +49,14 @@ cleanDIANNChunk = function(input, output_path, MBR, quantificationColumn, pos,
                            qvalue_cutoff = 0.01,
                            pg_qvalue_cutoff = 0.01) {
     input = MSstatsImport(list(input = input),
-                                          "MSstats", "DIANN")
+                          "MSstats", "DIANN")
     input = MSstatsClean(
-        input, MBR, quantificationColumn
-        #Todo: Add , global_qvalue_cutoff, qvalue_cutoff, pg_qvalue_cutoff params
+        input, 
+        MBR = MBR, 
+        quantificationColumn = quantificationColumn,
+        global_qvalue_cutoff = global_qvalue_cutoff, 
+        qvalue_cutoff = qvalue_cutoff,
+        pg_qvalue_cutoff = pg_qvalue_cutoff
     )
     .writeChunkToFile(input, output_path, pos)
     NULL

R/clean_DIANN.R

@@ -158,10 +158,7 @@ bigSpectronauttoMSstatsFormat <-  function(input_file, output_file_name,
 #' Convert out-of-memory DIANN files to MSstats format.
 #'
 #' @inheritParams MSstatsPreprocessBig
-#' @param MBR True if analysis was done with match between runs.
-#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
-#' Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. 
-#' Use 'auto' for quantified intensities for DIANN 2.0+
+#' @inheritParams MSstatsConvert::DIANNtoMSstatsFormat
 #'
 #' @export
 #'
@@ -173,6 +170,9 @@ bigDIANNtoMSstatsFormat <- function(input_file,
                                     backend,
                                     MBR = TRUE,
                                     quantificationColumn = "FragmentQuantCorrected",
+                                    global_qvalue_cutoff = 0.01,
+                                    qvalue_cutoff = 0.01,
+                                    pg_qvalue_cutoff = 0.01,
                                     max_feature_count = 100,
                                     filter_unique_peptides =  FALSE,
                                     aggregate_psms =  FALSE,
@@ -186,7 +186,8 @@ bigDIANNtoMSstatsFormat <- function(input_file,
   reduceBigDIANN(input_file, 
                  paste0("reduce_output_", output_file_name),
                  MBR,
-                 quantificationColumn)
+                 quantificationColumn,
+                 global_qvalue_cutoff, qvalue_cutoff, pg_qvalue_cutoff)
 
   # Preprocess the cleaned data (feature selection, etc.)
   msstats_data <- MSstatsPreprocessBig(