From 4973d7dab4817800468078a2822aebc8989a2a07 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 30 Apr 2026 17:49:54 -0400
Subject: [PATCH 1/2] fix bug for inf fc

---
 R/utils_getSubnetworkFromIndra.R              |  2 ++
 .../test-utils_getSubnetworkFromIndra.R       | 32 +++++++++++++++++++
 2 files changed, 34 insertions(+)

diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index ef14ef2..089ff93 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -166,6 +166,8 @@
     infinite_fc_proteins <- NULL
     if (include_infinite_fc) {
         infinite_fc_proteins <- input[is.infinite(input$log2FC), ]
+    } else {
+        input <- input[!is.infinite(input$log2FC), ]
     }
 
     input <- input[!is.na(input$adj.pvalue),]
diff --git a/tests/testthat/test-utils_getSubnetworkFromIndra.R b/tests/testthat/test-utils_getSubnetworkFromIndra.R
index afd76db..a3e15b9 100644
--- a/tests/testthat/test-utils_getSubnetworkFromIndra.R
+++ b/tests/testthat/test-utils_getSubnetworkFromIndra.R
@@ -196,6 +196,38 @@ describe(".filterGetSubnetworkFromIndraInput", {
         )
         expect_true("D" %in% result$Protein)
     })
+
+    test_that(".filterGetSubnetworkFromIndraInput excludes infinite FC proteins with adj.pvalue=0 when include_infinite_fc is FALSE", {
+        # MSstats sets adj.pvalue=0 for infinite FC proteins; they must still be excluded
+        input <- data.frame(
+            Protein   = c("A", "B", "D"),
+            log2FC    = c(3, -3, Inf),
+            adj.pvalue = c(0.01, 0.01, 0),
+            stringsAsFactors = FALSE
+        )
+        result <- MSstatsBioNet:::.filterGetSubnetworkFromIndraInput(
+            input, pvalueCutoff = 0.05, logfc_cutoff = NULL,
+            force_include_other = NULL, include_infinite_fc = FALSE, direction = "both"
+        )
+        expect_false("D" %in% result$Protein)
+    })
+
+    test_that(".filterGetSubnetworkFromIndraInput includes infinite FC protein via force_include_other even when include_infinite_fc is FALSE", {
+        input <- cbind(
+            data.frame(
+                Protein   = c("A", "B", "D"),
+                log2FC    = c(3, -3, Inf),
+                adj.pvalue = c(0.01, 0.01, 0),
+                stringsAsFactors = FALSE
+            ),
+            HgncId = c("1", "2", "4")
+        )
+        result <- MSstatsBioNet:::.filterGetSubnetworkFromIndraInput(
+            input, pvalueCutoff = 0.05, logfc_cutoff = NULL,
+            force_include_other = c("HGNC:4"), include_infinite_fc = FALSE, direction = "both"
+        )
+        expect_true("D" %in% result$Protein)
+    })
     
     test_that(".filterGetSubnetworkFromIndraInput filters by direction up", {
         result <- MSstatsBioNet:::.filterGetSubnetworkFromIndraInput(

From d1d3178ffa7b5b2c4da400c25c485aecc3a40411 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 30 Apr 2026 23:25:34 -0400
Subject: [PATCH 2/2] adjust infinite fold change filter to only happen if
 log2FC is a column

---
 .Rbuildignore                    | 2 ++
 .gitignore                       | 1 +
 R/utils_getSubnetworkFromIndra.R | 4 +++-
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index cc0e547..8e51b6c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -7,3 +7,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.positai$
+^\.claude$
diff --git a/.gitignore b/.gitignore
index 8960620..047cf71 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@
 /doc/
 /Meta/
 docs
+.positai
diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index 089ff93..760b1f6 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -167,7 +167,9 @@
     if (include_infinite_fc) {
         infinite_fc_proteins <- input[is.infinite(input$log2FC), ]
     } else {
-        input <- input[!is.infinite(input$log2FC), ]
+        if ("log2FC" %in% colnames(input)) {
+            input <- input[!is.infinite(input$log2FC), ]
+        }
     }
 
     input <- input[!is.na(input$adj.pvalue),]