Mercurial > repos > jiechenable1987 > qqq_test
view qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.R @ 0:8933ecfb6ab2 default tip
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author | jiechenable1987 |
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date | Fri, 24 Feb 2012 17:42:16 -0500 |
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#! /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)