Mercurial > repos > ethevenot > multivariate

annotate runit/multivariate_tests.R @ 4:5526f8258e8a draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3
author ethevenot
date Wed, 28 Feb 2018 09:59:25 -0500
parents fa173e12e185
children
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
diff changeset
1 test_input_pca <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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3 testDirC <- "input"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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4 argLs <- list(respC = "none",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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5 predI = "NA",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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6 orthoI = "0",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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7 testL = "FALSE")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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9 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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10 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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12 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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14 test_input_pcaGender <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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16 testDirC <- "input"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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17 argLs <- list(respC = "none",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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18 predI = "NA",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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19 orthoI = "0",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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20 testL = "FALSE",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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21 parMahalC = "gender")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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23 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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24 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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26 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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28 test_input_plsdaGender <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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30 testDirC <- "input"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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31 argLs <- list(respC = "gender",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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32 predI = "NA",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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33 orthoI = "0",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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34 testL = "FALSE")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
parents:
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36 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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37 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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39 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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41 test_input_oplsAge <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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43 testDirC <- "input"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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44 argLs <- list(respC = "age",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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45 predI = "1",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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46 orthoI = "1",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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47 testL = "FALSE")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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49 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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50 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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52 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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54 test_input_oplsdaGender <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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56 testDirC <- "input"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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57 argLs <- list(respC = "gender",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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58 predI = "1",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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59 orthoI = "1",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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60 testL = "FALSE")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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62 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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63 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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65 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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67 test_sacurine_pca <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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69 testDirC <- "sacurine"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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70 argLs <- list(respC = "none",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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71 predI = "NA",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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72 orthoI = "0",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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73 testL = "FALSE")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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ethevenot
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75 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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76 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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78 }
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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80 test_sacurine_pcaGender <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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82 testDirC <- "sacurine"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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83 argLs <- list(respC = "none",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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84 predI = "NA",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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85 orthoI = "0",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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86 testL = "FALSE",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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87 parMahalC = "gender")
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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88
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ethevenot
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89 argLs <- c(defaultArgF(testDirC), argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
parents:
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90 outLs <- wrapperCallF(argLs)
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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92 }
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94 test_sacurine_plsAge <- function() {
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
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96 testDirC <- "sacurine"
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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97 argLs <- list(respC = "age",
fa173e12e185 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
ethevenot
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98 predI = "NA",
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99 orthoI = "0",
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100 testL = "FALSE")
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101
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102 argLs <- c(defaultArgF(testDirC), argLs)
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parents:
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103 outLs <- wrapperCallF(argLs)
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104
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105 }
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106
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parents:
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107 test_sacurine_plsdaGender <- function() {
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108
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109 testDirC <- "sacurine"
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110 argLs <- list(respC = "gender",
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111 predI = "NA",
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112 orthoI = "0",
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113 testL = "FALSE")
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114
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115 argLs <- c(defaultArgF(testDirC), argLs)
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116 outLs <- wrapperCallF(argLs)
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117
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118 }
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119
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120 test_sacurineTest_pls <- function() {
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121
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122 testDirC <- "sacurineTest"
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123 argLs <- list(respC = "age",
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124 predI = "2",
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125 orthoI = "0",
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126 testL = "TRUE")
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127
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128 argLs <- c(defaultArgF(testDirC), argLs)
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129 outLs <- wrapperCallF(argLs)
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130
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131 checkEqualsNumeric(outLs[["samDF"]][181, "age_PLS_predictions"], 40.82252, tolerance = 1e-5)
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132
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133 }
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134
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135 test_sacurineTest_opls <- function() {
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136
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137 testDirC <- "sacurineTest"
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138 argLs <- list(respC = "age",
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139 predI = "1",
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140 orthoI = "2",
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141 testL = "TRUE")
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142
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143 argLs <- c(defaultArgF(testDirC), argLs)
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144 outLs <- wrapperCallF(argLs)
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145
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parents:
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146 checkEqualsNumeric(outLs[["samDF"]][181, "age_OPLS_predictions"], 40.28963, tolerance = 1e-5)
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147
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148 }
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149
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150 test_sacurineTest_plsda <- function() {
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151
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152 testDirC <- "sacurineTest"
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153 argLs <- list(respC = "gender",
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154 predI = "2",
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155 orthoI = "0",
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156 testL = "TRUE")
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157
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158 argLs <- c(defaultArgF(testDirC), argLs)
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159 outLs <- wrapperCallF(argLs)
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160
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161 checkEquals(outLs[["samDF"]][181, "gender_PLSDA_predictions"], "F")
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162
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163 }
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164
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165 test_sacurineTest_oplsda <- function() {
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166
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167 testDirC <- "sacurineTest"
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168 argLs <- list(respC = "gender",
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169 predI = "1",
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170 orthoI = "1",
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171 testL = "TRUE")
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172
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173 argLs <- c(defaultArgF(testDirC), argLs)
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174 outLs <- wrapperCallF(argLs)
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175
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176 checkEquals(outLs[["samDF"]][181, "gender_OPLSDA_predictions"], "F")
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177
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178 }
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179
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180 test_sacurine_oplsAge <- function() {
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181
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182 testDirC <- "sacurine"
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183 argLs <- list(respC = "age",
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184 predI = "1",
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185 orthoI = "1",
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186 testL = "FALSE")
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187
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188 argLs <- c(defaultArgF(testDirC), argLs)
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189 outLs <- wrapperCallF(argLs)
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190
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191 checkEqualsNumeric(outLs[["varDF"]][1, "age_OPLS_VIP_ortho"], 0.3514378, tolerance = 1e-7)
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192 }
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193
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194 test_example1_plsda <- function() {
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195
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196 testDirC <- "example1"
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parents:
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197 argLs <- list(respC = "traitment",
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ethevenot
parents:
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198 predI = "3",
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ethevenot
parents:
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199 orthoI = "0",
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ethevenot
parents:
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200 testL = "FALSE")
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ethevenot
parents:
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201
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ethevenot
parents:
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202 argLs <- c(defaultArgF(testDirC), argLs)
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ethevenot
parents:
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203 outLs <- wrapperCallF(argLs)
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ethevenot
parents:
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204
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ethevenot
parents:
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205 }
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ethevenot
parents:
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206
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ethevenot
parents:
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207 test_example2_pca <- function() {
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ethevenot
parents:
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208
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ethevenot
parents:
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209 testDirC <- "example2"
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ethevenot
parents:
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210 argLs <- list(respC = "none",
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ethevenot
parents:
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211 predI = "NA",
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ethevenot
parents:
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212 orthoI = "0",
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ethevenot
parents:
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213 testL = "FALSE")
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ethevenot
parents:
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214
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ethevenot
parents:
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215 argLs <- c(defaultArgF(testDirC), argLs)
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ethevenot
parents:
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216 outLs <- wrapperCallF(argLs)
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ethevenot
parents:
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217
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ethevenot
parents:
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218 }