--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_checkpanel.R	Tue Jul 27 21:47:56 2021 +0000
@@ -0,0 +1,37 @@
+#!/usr/bin/env Rscript
+######################################################################
+#                  Copyright (c) 2018 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1 - January 2018
+# Author: Cristel Thomas
+#
+#
+
+library(MetaCyto)
+
+check_panel <- function(df, outfile = "") {
+  report <- panelSummary(df, ".", cluster = F, width = 30, height = 20)
+  markers <- data.frame("Markers" = row.names(report))
+  s <- cbind(markers, report)
+  write.table(s, file = outfile, quote = F, row.names = F, col.names = T, sep = "\t")
+}
+
+check_input_format <- function(infile = "", outfile = "") {
+  df <- read.table(infile, sep = "\t", header = T, colClasses = "character")
+  nm <- colnames(df)
+  check_ab <- if ("antibodies" %in% nm) TRUE else FALSE
+  check_sdy <- if ("study_id" %in% nm) TRUE else FALSE
+
+  if (check_sdy && check_ab) {
+    check_panel(df, outfile)
+  } else {
+    quit(save = "no", status = 10, runLast = FALSE)
+  }
+}
+
+################################################################################
+args <- commandArgs(trailingOnly = TRUE)
+
+check_input_format(args[1], args[2])