Maaslin2 Typo Modify

R/compare_daa_results.R

@@ -27,15 +27,25 @@
 #' data("metadata")
 #'
 #' # Run pathway_daa function for multiple methods
-#' methods <- c("ALDEx2", "DESeq2", "edgeR")
+#' methods <- c("ALDEx2", "DESeq2", "edgeR","Maaslin2")
 #' daa_results_list <- lapply(methods, function(method) {
 #' pathway_daa(abundance = metacyc_abundance %>% column_to_rownames("pathway"),
 #' metadata = metadata, group = "Environment", daa_method = method)
 #' })
 #'
+#' names(daa_results_list) <- methods
+#' # Correct Maaslin2 feature names by replacing dots with hyphens.
+#' # Note: When using Maaslin2 as the differential abundance analysis method,
+#' # it modifies the original feature names by replacing hyphens (-) with dots (.).
+#' # This replacement can cause inconsistencies when trying to compare results from Maaslin2
+#' # with those from other methods that do not modify feature names.
+#' # Therefore, this line of code reverses that replacement, converting the dots back into
+#' # hyphens for accurate and consistent comparisons across different methods.
+#' daa_results_list[["Maaslin2"]]$feature <- gsub("\\.", "-", daa_results_list[["Maaslin2"]]$feature)
+#'
 #' # Compare results across different methods
 #' comparison_results <- compare_daa_results(daa_results_list = daa_results_list,
-#' method_names = c("ALDEx2_Welch's t test","ALDEx2_Wilcoxon rank test","DESeq2", "edgeR"))
+#' method_names = c("ALDEx2_Welch's t test","ALDEx2_Wilcoxon rank test","DESeq2", "edgeR", "Maaslin2"))
 #' }
 #' @export
 utils::globalVariables(c("group1","group2"))