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Migrated tool version 1.0 from old tool shed archive to new tool shed repository
author andreu
date Tue, 07 Jun 2011 17:26:58 -0400
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55561a945415 Migrated tool version 1.0 from old tool shed archive to new tool shed repository
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1 #! /soft/general/R-2.13.0/bin/Rscript
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2 rm(list=ls(all=TRUE))
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3
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4 ########################################################################
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5 # HumMeth27QCReport.R a parser of the HumMeth27QCReport R package
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6 # Copyright (C) 2011 Andreu Alibes (aalibes@gmail.com)
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7 #
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8 # This program is free software: you can redistribute it and/or modify
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9 # it under the terms of the GNU General Public License as published by
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10 # the Free Software Foundation, either version 3 of the License, or
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11 # (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful,
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14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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16 # GNU General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 ########################################################################
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21
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23
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24 ##First read in the arguments listed at the command line
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25 args=(commandArgs(TRUE))
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26
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27 ##args is now a list of character vectors
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28 ## First check to see if arguments are passed.
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29 ## Then cycle through each element of the list and evaluate the expressions.
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30 if(length(args)==0){
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31 print("No arguments supplied.")
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32 ##supply default values
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33 Directory = ""
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34 Plat = ""
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35 pvalue = ""
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36 chrom = ""
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37 method = ""
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38 } else {
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39 # print(args)
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40 for(i in 1:length(args)){
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41 eval(parse(text=args[[i]]))
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42 }
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43 }
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44
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45 library("HumMeth27QCReport")
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46 Dir <- Directory
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47 ImportDataR <- ImportData(Dir)
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48 normMvalues <- HumMeth27QCReport(ImportDataR, platform = Plat, pval = pvalue, ChrX = chrom, ClustMeth=method)