From 6696332be37882874620895801374f595178af67 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 4 Apr 2025 18:54:43 -0400
Subject: [PATCH 1/3] fix(pd-converter): Remove QuanInfo column after cleaning
 up PD data

---
 R/clean_ProteomeDiscoverer.R                  | 1 +
 inst/tinytest/test_cleanRaw.R                 | 2 +-
 inst/tinytest/test_clean_ProteomeDiscoverer.R | 3 +--
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/clean_ProteomeDiscoverer.R b/R/clean_ProteomeDiscoverer.R
index 4feba663..a676a819 100644
--- a/R/clean_ProteomeDiscoverer.R
+++ b/R/clean_ProteomeDiscoverer.R
@@ -131,6 +131,7 @@
       pd_input = pd_input[toupper(QuanInfo) == 'UNIQUE', ]
     }
   }
+  pd_input = pd_input[, setdiff(colnames(pd_input), c("QuanInfo")), with = FALSE]
   pd_input
 }
 
diff --git a/inst/tinytest/test_cleanRaw.R b/inst/tinytest/test_cleanRaw.R
index aadf08be..e5e63e98 100644
--- a/inst/tinytest/test_cleanRaw.R
+++ b/inst/tinytest/test_cleanRaw.R
@@ -146,7 +146,7 @@ expect_error(MSstatsConvert::MSstatsClean(pdtmt_import,
                                           remove_shared = TRUE,
                                           intensity_columns_regexp = "Nothing"))
 expect_equal(
-    ncol(pdtmt_cleaned), 11
+    ncol(pdtmt_cleaned), 10
 )
 expect_true(nrow(pdtmt_cleaned) > 0)
 # Progenesis
diff --git a/inst/tinytest/test_clean_ProteomeDiscoverer.R b/inst/tinytest/test_clean_ProteomeDiscoverer.R
index 4d88f0e7..c6c03f74 100644
--- a/inst/tinytest/test_clean_ProteomeDiscoverer.R
+++ b/inst/tinytest/test_clean_ProteomeDiscoverer.R
@@ -1,6 +1,6 @@
 .testHappyPath = function(input) {
     output = MSstatsConvert:::.cleanRawPDTMT(input)
-    expect_equal(ncol(output), 11)
+    expect_equal(ncol(output), 10)
     expect_true(nrow(output) > 0)
     expected_column_names = c(
         "ProteinName",
@@ -9,7 +9,6 @@
         "PrecursorCharge",
         "IonsScore",
         "Run",
-        "QuanInfo",
         "IsolationInterference",
         "PSM",
         "Channel",

From 18ffaf17cb9ff551b16f7623b10e4e84a6f04d6c Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 4 Apr 2025 19:13:56 -0400
Subject: [PATCH 2/3] make code look nicer

---
 R/clean_ProteomeDiscoverer.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clean_ProteomeDiscoverer.R b/R/clean_ProteomeDiscoverer.R
index a676a819..0dd6e33c 100644
--- a/R/clean_ProteomeDiscoverer.R
+++ b/R/clean_ProteomeDiscoverer.R
@@ -131,7 +131,7 @@
       pd_input = pd_input[toupper(QuanInfo) == 'UNIQUE', ]
     }
   }
-  pd_input = pd_input[, setdiff(colnames(pd_input), c("QuanInfo")), with = FALSE]
+  pd_input = pd_input[, !(colnames(pd_input) %in% "QuanInfo")]
   pd_input
 }
 

From 71e57c9f139a8d4c05d7584406f29ca740e59731 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 4 Apr 2025 19:32:12 -0400
Subject: [PATCH 3/3] fix bug

---
 R/clean_ProteomeDiscoverer.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clean_ProteomeDiscoverer.R b/R/clean_ProteomeDiscoverer.R
index 0dd6e33c..2f3e5992 100644
--- a/R/clean_ProteomeDiscoverer.R
+++ b/R/clean_ProteomeDiscoverer.R
@@ -131,7 +131,7 @@
       pd_input = pd_input[toupper(QuanInfo) == 'UNIQUE', ]
     }
   }
-  pd_input = pd_input[, !(colnames(pd_input) %in% "QuanInfo")]
+  pd_input = pd_input[, !(colnames(pd_input) %in% "QuanInfo"), with = FALSE]
   pd_input
 }