--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.R	Fri Feb 24 17:42:16 2012 -0500
@@ -0,0 +1,48 @@
+#! /soft/general/R-2.13.0/bin/Rscript 
+rm(list=ls(all=TRUE))
+
+########################################################################
+# HumMeth27QCReport.R a parser of the HumMeth27QCReport R package
+# Copyright (C) 2011  Andreu Alibes (aalibes@gmail.com)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+########################################################################
+
+
+
+##First read in the arguments listed at the command line
+args=(commandArgs(TRUE))
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    Directory = ""
+    Plat = ""
+    pvalue = ""
+    chrom = ""
+    method = ""
+} else {
+#   print(args)
+    for(i in 1:length(args)){
+         eval(parse(text=args[[i]]))
+    }
+}
+
+library("HumMeth27QCReport")
+Dir <- Directory
+ImportDataR <- ImportData(Dir)
+normMvalues <- HumMeth27QCReport(ImportDataR, platform = Plat, pval = pvalue, ChrX = chrom, ClustMeth=method)