Mercurial > repos > marie-tremblay-metatoul > normalization

annotate NmrNormalization_wrapper.R @ 6:221cbd549c40 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
author workflow4metabolomics
date Tue, 30 Jul 2019 09:43:57 -0400
parents 3d00a98974b7
children
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1 #!/usr/bin/env Rscript
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3 ## 070115_NmrBucketing2galaxy_v1.R
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
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6 ## www.metabohub.fr/en
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7 ## marie.tremblay-franco@toulouse.inra.fr
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9 runExampleL <- FALSE
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12 ##------------------------------
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13 ## Options
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14 ##------------------------------
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15 strAsFacL <- options()$stringsAsFactors
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16 options(stringsAsFactors = FALSE)
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17 options(scipen=999)
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20 ##------------------------------
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21 ## Libraries laoding
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22 ##------------------------------
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23 # For parseCommandArgs function
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24 library(batch)
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26 # Constants
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27 argv <- commandArgs(trailingOnly = FALSE)
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28 script.path <- sub("--file=","",argv[grep("--file=",argv)])
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29 prog.name <- basename(script.path)
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31 # Print help
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32 if (length(grep('-h', argv)) >0) {
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33 cat("Usage:", prog.name,
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34 "dataMatrix myDataMatrix.tsv",
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35 "scalingMethod PQN|QuantitativeVariable",
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36 "graphType None|Overlay|One_per_individual",
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37 "logOut myLog.txt",
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38 "dataMatrixOut myDataMatrixOutput.tsv",
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39 "graphOut myGraph.pdf",
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40 "\n")
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41 quit(status = 0)
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42 }
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44 # R script call
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45 source_local <- function(fname)
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46 {
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47 argv <- commandArgs(trailingOnly = FALSE)
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48 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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49 source(paste(base_dir, fname, sep="/"))
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50 }
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51 #Import the different functions
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52 source_local("NmrNormalization_script.R")
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53 source_local("DrawSpec.R")
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56 ##------------------------------
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57 ## Errors ?????????????????????
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58 ##------------------------------
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61 ##------------------------------
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62 ## Constants
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63 ##------------------------------
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64 topEnvC <- environment()
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65 flagC <- "\n"
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68 ##------------------------------
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69 ## Script
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70 ##------------------------------
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71 if(!runExampleL)
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72 argLs <- parseCommandArgs(evaluate=FALSE)
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75 ## Parameters Loading
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76 ##-------------------
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77 # Inputs
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78 data <- read.table(argLs[["dataMatrix"]], check.names=FALSE, header=TRUE, sep="\t", row.names=1)
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79 names <- rownames(data)
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80 ## Add a test to check if all values are numercical
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81 if (!all(vapply(data, is.numeric, FUN.VALUE = FALSE)))
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82 stop("Data are not numeric")
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83 ## Integer conversion to avoid stack overflow when computin the sum
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84 data <- as.data.frame(lapply(data, as.numeric))
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85 rownames(data) <- names
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86
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87 scaling <- argLs[["scalingMethod"]]
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88 graphique <- argLs[["graphType"]]
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90 if (scaling=='PQN')
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91 {
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92 metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
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93 factor<- argLs[["factor"]]
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94 ControlGroup <- argLs[["controlGroup"]]
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95 }
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96 if (scaling=='QuantitativeVariable')
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97 {
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98 metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
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99 factor <- argLs[["factor"]]
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100 }
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101
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102 # Outputs
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103 nomGraphe <- argLs[["graphOut"]]
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104 dataMatrixOut <- argLs[["dataMatrixOut"]]
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105 log <- argLs[["logOut"]]
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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106
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107
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108 ## Checking R packages
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109 ##--------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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110 sink(log)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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111 cat("\tPACKAGE INFO\n")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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112 pkgs=c("batch")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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113 for(pkg in pkgs) {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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114 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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115 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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116 }
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117 cat("\n")
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118
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119
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120 ## Checking arguments
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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121 ##-------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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122 error.stock <- "\n"
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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123 if(length(error.stock) > 1)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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124 stop(error.stock)
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125
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126
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127 ## Computation
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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128 ##------------
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129 NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample,
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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130 bioFactor=factor,ControlGroup=ControlGroup,
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131 graph=graphique,nomFichier=nomGraphe,savLog.txtC=log)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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132
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133 data_normalized <- NormalizationResults[[1]]
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134
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135
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136 ## Graphical outputs
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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137 ##------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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138 if (graphique != "None")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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139 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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140 # Graphic Device opening
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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141 pdf(nomGraphe,onefile=TRUE)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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142
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143 if (graphique == "Overlay")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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144 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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145 # Global spectral window
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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146 spectra <- data.frame(t(data_normalized))
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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147 drawSpec(spectra,xlab="", ylab="Intensity", main="")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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148 }
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149 else
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150 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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151 for (i in 1:ncol(data_normalized))
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152 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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153 spectra <- t(data_normalized[,i])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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154 drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_normalized)[i])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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155 }
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156 }
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157 dev.off()
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158 }
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159
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160
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161 ## Saving
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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162 ##-------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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163 # Data
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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164 data_normalized <- cbind(rownames(data_normalized),data_normalized)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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165 colnames(data_normalized) <- c("Variable",colnames(data_normalized)[-1])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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166 write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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167
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168
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169 ## Ending
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170 ##---------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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171 cat("\nEnd of 'Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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172 sink()
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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173 options(stringsAsFactors = strAsFacL)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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174 rm(list = ls())