fix issue of site level report in over representation test

Author: hsiaoyi0504

R/enrichment.R

@@ -135,7 +135,7 @@ or_test <- function(se, database="GO Biological Process", backend="enrichr", dir
           genes <- unique(significant$Gene)
         } else if (metadata(dep)$level == "protein" | metadata(dep)$level == "gene") {
           genes <- significant$name
-        } else if (metadata(dep)$level == "peptide") {
+        } else if (metadata(dep)$level %in% c("peptide", "site")) {
           genes <- unique(significant$Gene)
         }
 
@@ -446,7 +446,7 @@ test_ora_mod <- function(dep,
     background <- unique(row_data$ID)
   } else if (metadata(dep)$level == "protein") {
     background <- unique(gsub("[.].*", "", row_data$name))
-  } else if (metadata(dep)$level == "peptide") {
+  } else if (metadata(dep)$level %in% c("peptide", "site")) {
     background <- unique(row_data$Gene)
   }
 
@@ -495,7 +495,7 @@ test_ora_mod <- function(dep,
         genes <- unique(significant$ID)
       } else if (metadata(dep)$level == "protein") {
         genes <- significant$name
-      } else if (metadata(dep)$level == "peptide") {
+      } else if (metadata(dep)$level %in% c("peptide", "site")) {
         genes <- unique(significant$Gene)
       }
 

R/io.R

@@ -307,11 +307,13 @@ make_se_from_files <- function(quant_table_path, exp_anno_path, type = "TMT", le
                                              "Gene", "ProteinID", "Peptide", "SequenceWindow", additional_cols)))
       }
       # test_match_DIA_column_design(data_unique, selected_cols, exp_design)
-      data_se <- make_se_customized(data_unique, selected_cols, exp_design, log2transform=log2transform, exp="DIA", level="peptide")
+      data_se <- make_se_customized(data_unique, selected_cols, exp_design, log2transform=log2transform, exp="DIA", level=level)
       dimnames(data_se) <- list(dimnames(data_se)[[1]], colData(data_se)$sample_name)
       colData(data_se)$label <- colData(data_se)$sample_name
     }
-    rowData(data_se)$Gene <- rowData(data_se)$Genes
+    if (level == "peptide") {
+      rowData(data_se)$Gene <- rowData(data_se)$Genes
+    }
   } else { # TMT
     temp_exp_design <- exp_design
     # sample without specified condition will be removed