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annotate checkformat_script.R @ 5:e7c5811ec12f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 6b7aa0db6cebdb8acfac0a07291647947260a310
author ethevenot
date Thu, 01 Mar 2018 05:07:38 -0500
parents 9590fac86f63
children
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e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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1 ## Etienne Thevenot
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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2 ## CEA, MetaboHUB Paris
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3 ## etienne.thevenot@cea.fr
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7 ## Reads the dataMatrix, sampleMetadata, and variableMetadata .tsv files
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8 ## and checks the formats
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9 readAndCheckF <- function(datFilC="dataMatrix.tsv",
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10 samFilC="sampleMetadata.tsv",
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11 varFilC="variableMetadata.tsv",
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12 makNamL) {
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15 ## options
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17 optStrAsFacL <- options()[["stringsAsFactors"]]
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18 options(stringsAsFactors = FALSE)
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21 ## checking that the tables have no duplicated row or column names
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23 for(tabC in c("dat", "sam", "var")) {
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25 tabNamC <- switch(tabC, dat="dataMatrix", sam="sampleMetadata", var="variableMetadata")
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27 rowVc <- read.table(eval(parse(text=paste0(tabC, "FilC"))),
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28 check.names = FALSE,
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29 header = TRUE,
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30 sep = "\t")[, 1]
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32 colVc <- unlist(read.table(eval(parse(text=paste0(tabC, "FilC"))),
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33 check.names = FALSE,
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34 nrow=1,
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35 sep = "\t"))[-1]
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37 if(any(duplicated(rowVc)))
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38 stop("The following row name(s) is/are duplicated in the ",
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39 tabNamC,
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40 " table: '",
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41 paste(rowVc[duplicated(rowVc)], collapse="', '"), "'",
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42 call.=FALSE)
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44 if(any(duplicated(colVc)))
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45 stop("The following column name(s) is/are duplicated in the ",
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46 tabNamC,
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47 " table: '",
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48 paste(colVc[duplicated(colVc)], collapse="', '"), "'",
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49 call.=FALSE)
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51 }
3
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52
1
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53
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54 ## reading tables
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56 datMN <- t(as.matrix(read.table(datFilC,
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57 check.names = FALSE,
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58 header = TRUE,
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59 row.names = 1,
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60 sep = "\t")))
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61
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62 samDF <- read.table(samFilC,
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63 check.names = FALSE,
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64 header = TRUE,
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65 row.names = 1,
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66 sep = "\t")
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67
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68 varDF <- read.table(varFilC,
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69 check.names = FALSE,
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70 header = TRUE,
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71 row.names = 1,
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72 sep = "\t")
3
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1
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74
3
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75 ## checking that dataMatrix is numeric and that the sample and variable numbers are coherent
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77 if(mode(datMN) != "numeric") {
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78 stop("The dataMatrix is not of the 'numeric' type",
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79 call. = FALSE)
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80 }
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81
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82 if(nrow(datMN) != nrow(samDF)) {
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83 if(nrow(datMN) > nrow(samDF)) {
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84 print(setdiff(rownames(datMN), rownames(samDF)))
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85 stop("The sample names above from dataMatrix were not found in sampleMetadata",
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86 call. = FALSE)
3
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87 } else {
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88 print(setdiff(rownames(samDF), rownames(datMN)))
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89 stop("The sample names above from sampleMetadata were not found in dataMatrix",
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90 call. = FALSE)
3
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91 }
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92 }
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93
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94 if(ncol(datMN) != nrow(varDF)) {
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95 if(ncol(datMN) > nrow(varDF)) {
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96 print(setdiff(colnames(datMN), rownames(varDF)))
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97 stop("The variable names above from dataMatrix were not found in variableMetadata",
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98 call. = FALSE)
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99 } else {
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100 print(setdiff(rownames(varDF), colnames(datMN)))
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101 stop("The variable names above from variableMetadata were not found in dataMatrix",
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102 call. = FALSE)
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103 }
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104 }
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105
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106
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107 ## making sample and variable names (optional)
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108
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109 newL <- FALSE
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110
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111 if(makNamL) {
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112
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113 cat("\n\nMessage: Converting sample and variable names to the standard R format\n")
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114
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115 rownames(datMN) <- make.names(rownames(datMN), unique = TRUE)
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116 colnames(datMN) <- make.names(colnames(datMN), unique = TRUE)
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117 rownames(samDF) <- make.names(rownames(samDF), unique = TRUE)
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118 rownames(varDF) <- make.names(rownames(varDF), unique = TRUE)
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119
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120 newL <- TRUE
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121
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122 }
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123
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124
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125 ## checking sample and variable names
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126
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127 chkL <- TRUE
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128
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129 if(!identical(rownames(datMN), rownames(samDF))) {
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130
3
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131 if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
1
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132
3
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133 cat("\n\nMessage: Re-ordering dataMatrix sample names to match sampleMetadata\n")
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134 datMN <- datMN[rownames(samDF), , drop = FALSE]
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135
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136 stopifnot(identical(sort(rownames(datMN)), sort(rownames(samDF))))
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137
3
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138 newL <- TRUE
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139
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140 } else {
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141
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142 cat("\n\nStop: The sample names of dataMatrix and sampleMetadata do not match:\n")
1
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143 print(cbind.data.frame(indice = 1:nrow(datMN),
3
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144 dataMatrix=rownames(datMN),
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145 sampleMetadata=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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146 chkL <- FALSE
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147
1
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148 }
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149
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150 }
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151
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152 if(!identical(colnames(datMN), rownames(varDF))) {
3
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153
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154 if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) {
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155
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156 cat("\n\nMessage: Re-ordering dataMatrix variable names to match variableMetadata\n")
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157 datMN <- datMN[, rownames(varDF), drop = FALSE]
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158
3
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159 stopifnot(identical(sort(colnames(datMN)), sort(rownames(varDF))))
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160
3
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161 newL <- TRUE
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162
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163 } else {
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164
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165 cat("\n\nStop: The variable names of dataMatrix and variableMetadata do not match:\n")
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166 print(cbind.data.frame(indice = 1:ncol(datMN),
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167 dataMatrix=colnames(datMN),
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168 variableMetadata=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
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169 chkL <- FALSE
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170
1
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171 }
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172
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173 }
3
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174
1
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175
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176 options(stringsAsFactors=optStrAsFacL)
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177
3
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178 resLs <- list(chkL=chkL,
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179 newL = newL,
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180 datMN = datMN,
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181 samDF = samDF,
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182 varDF = varDF)
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183
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184 return(resLs)
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185
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186 } ## end of checkAndReadF
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187