From 5b887fff711b09e572c9fba10f4e517fdc16fceb Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Mon, 23 Sep 2024 12:57:30 +0200
Subject: [PATCH] quick update

---
 R/MsExperiment.R | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/R/MsExperiment.R b/R/MsExperiment.R
index 2ffff28..66bdba2 100644
--- a/R/MsExperiment.R
+++ b/R/MsExperiment.R
@@ -253,7 +253,6 @@ setMethod("readMsObject",
               # merging
               ord <- match(assay_data$`Sample Name`, sample_info$`Sample Name`)
               merged_data <- cbind(assay_data, sample_info[ord, ])
-              names(merged_data) <- gsub(" ", "_", names(merged_data))
               if (keepProtocol || keepOntology || simplify)
                   merged_data <- .clean_merged(x = merged_data,
                                                keepProtocol = keepProtocol,
@@ -284,18 +283,9 @@ setMethod("readMsObject",
 
 #####HELPERS
 
-#' function that takes the extra parameters and clean the metadata if asked by
+#' Function that takes the extra parameters and clean the metadata if asked by
 #' the user.
 #'
-#' Note:  the subsetting of the merged data is done here, which WILL rename the
-#' duplicated columns. I could fix that by first transforming the data.frame into
-#' a list but I am not sure that it is useful.. The user might do some
-#' subsetting too later and then the same thing will happen. Might as well have
-#' it from the beginning.
-#'
-#' Note2: I would move that function later, keeping it her for review to help
-#' clarity
-#'
 #' @noRd
 .clean_merged <- function(x, keepProtocol, keepOntology, simplify) {
     # remove ontology