Merge pull request #175 from cfbeuchel/colheader_harmonisation_improv…

…ements

Add checks to standardise_sumstats_column_headers_crossplatform()

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")