Mercurial > repos > andreu > qcma
diff HumMeth27QCReport/HumMeth27QCReport.R @ 0:55561a945415 default tip
Migrated tool version 1.0 from old tool shed archive to new tool shed repository
author | andreu |
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date | Tue, 07 Jun 2011 17:26:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/HumMeth27QCReport/HumMeth27QCReport.R Tue Jun 07 17:26:58 2011 -0400 @@ -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)