From 61c5703f718f8caf9f563f89ccb1635fdeee3e52 Mon Sep 17 00:00:00 2001
From: cfbeuchel <carl.beuchel@charite.de>
Date: Fri, 9 Feb 2024 09:05:00 +0100
Subject: [PATCH] Add checks to
 standardise_sumstats_column_headers_crossplatform()

* Ensure mapping_file is a DF
* Change all entries in custom mapping_file to upper case
---
 ...dardise_sumstats_column_headers_crossplatform.R | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/R/standardise_sumstats_column_headers_crossplatform.R b/R/standardise_sumstats_column_headers_crossplatform.R
index 34a1749..12d9432 100644
--- a/R/standardise_sumstats_column_headers_crossplatform.R
+++ b/R/standardise_sumstats_column_headers_crossplatform.R
@@ -14,7 +14,7 @@
 #' @return list containing sumstats_dt, the modified summary statistics data
 #' table object
 #' @export
-#' @importFrom data.table setnames rbindlist
+#' @importFrom data.table setnames rbindlist setDF
 #' @examples
 #' sumstats_dt <- data.table::fread(system.file("extdata", "eduAttainOkbay.txt",
 #'                                              package = "MungeSumstats"))
@@ -24,7 +24,17 @@ standardise_header <- standardise_sumstats_column_headers_crossplatform <-
              mapping_file = sumstatsColHeaders,
              uppercase_unmapped=TRUE,
              return_list=TRUE) {
-          
+        
+        data.table::setDF(mapping_file)
+        if(!all.equal(
+            mapping_file, 
+            sumstatsColHeaders
+        )) {
+            message(
+                "Non-standard mapping file detected.",
+                "Making sure all entries in `Uncorrected` are in upper case.")
+            mapping_file$Uncorrected <- toupper(mapping_file$Uncorrected)
+        }
         message("Standardising column headers.")
         message("First line of summary statistics file: ")
         msg <- paste0(names(sumstats_dt), split = "\t")