fix bug for inf fc

.Rbuildignore

@@ -7,3 +7,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.positai$
+^\.claude$

.gitignore

@@ -8,3 +8,4 @@
 /doc/
 /Meta/
 docs
+.positai

R/utils_getSubnetworkFromIndra.R

@@ -166,6 +166,10 @@
     infinite_fc_proteins <- NULL
     if (include_infinite_fc) {
         infinite_fc_proteins <- input[is.infinite(input$log2FC), ]
+    } else {
+        if ("log2FC" %in% colnames(input)) {
+            input <- input[!is.infinite(input$log2FC), ]
+        }
     }
 
     input <- input[!is.na(input$adj.pvalue),]

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(