Mercurial > repos > ethevenot > multivariate

annotate runit/multivariate_tests.R @ 1:60c360e466a8 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 10:04:14 -0500
parents 4b9488602d57
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
1 test_input_pca <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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2
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
3 testDirC <- "input"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
4 argLs <- list(respC = "none",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
5 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
6 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
7 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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8
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
9 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
10 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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11
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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12 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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13
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
14 test_input_pcaGender <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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15
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
16 testDirC <- "input"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
17 argLs <- list(respC = "none",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
18 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
19 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
20 testL = "FALSE",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
21 parMahalC = "gender")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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22
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
23 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
24 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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25
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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26 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
28 test_input_plsdaGender <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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29
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
30 testDirC <- "input"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
31 argLs <- list(respC = "gender",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
32 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
33 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
34 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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35
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
36 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
37 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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38
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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39 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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40
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
41 test_input_oplsAge <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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42
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
43 testDirC <- "input"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
44 argLs <- list(respC = "age",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
45 predI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
46 orthoI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
47 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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48
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
49 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
50 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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51
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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52 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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parents:
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53
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
54 test_input_oplsdaGender <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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55
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
56 testDirC <- "input"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
57 argLs <- list(respC = "gender",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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58 predI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
59 orthoI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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60 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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61
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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62 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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63 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
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64
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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65 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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parents:
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66
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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67 test_sacurine_pca <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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68
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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69 testDirC <- "sacurine"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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70 argLs <- list(respC = "none",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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71 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
72 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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73 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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74
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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75 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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76 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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parents:
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77
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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78 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
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79
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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80 test_sacurine_pcaGender <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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81
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ethevenot
parents:
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82 testDirC <- "sacurine"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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83 argLs <- list(respC = "none",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
84 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
85 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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86 testL = "FALSE",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
87 parMahalC = "gender")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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88
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
89 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
90 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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91
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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92 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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93
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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94 test_sacurine_plsAge <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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95
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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96 testDirC <- "sacurine"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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97 argLs <- list(respC = "age",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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98 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
99 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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100 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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101
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ethevenot
parents:
diff changeset
102 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
103 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
104
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
105 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
106
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ethevenot
parents:
diff changeset
107 test_sacurine_plsdaGender <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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108
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ethevenot
parents:
diff changeset
109 testDirC <- "sacurine"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
110 argLs <- list(respC = "gender",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
111 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
112 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
113 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
114
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
115 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
116 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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117
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ethevenot
parents:
diff changeset
118 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
119
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
120 test_sacurineTest_pls <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
121
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
122 testDirC <- "sacurineTest"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
123 argLs <- list(respC = "age",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
124 predI = "2",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
125 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
126 testL = "TRUE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
127
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
128 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
129 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
130
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ethevenot
parents:
diff changeset
131 checkEqualsNumeric(outLs[["samDF"]][181, "age_PLS_predictions"], 40.82252, tolerance = 1e-5)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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132
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ethevenot
parents:
diff changeset
133 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
134
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ethevenot
parents:
diff changeset
135 test_sacurineTest_opls <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
136
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ethevenot
parents:
diff changeset
137 testDirC <- "sacurineTest"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
138 argLs <- list(respC = "age",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
139 predI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
140 orthoI = "2",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
141 testL = "TRUE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
142
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
143 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
144 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
145
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
146 checkEqualsNumeric(outLs[["samDF"]][181, "age_OPLS_predictions"], 40.28963, tolerance = 1e-5)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
147
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ethevenot
parents:
diff changeset
148 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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149
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ethevenot
parents:
diff changeset
150 test_sacurineTest_plsda <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
151
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ethevenot
parents:
diff changeset
152 testDirC <- "sacurineTest"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
153 argLs <- list(respC = "gender",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
154 predI = "2",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
155 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
156 testL = "TRUE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
157
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
158 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
159 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
160
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ethevenot
parents:
diff changeset
161 checkEquals(outLs[["samDF"]][181, "gender_PLSDA_predictions"], "F")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
162
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ethevenot
parents:
diff changeset
163 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
164
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ethevenot
parents:
diff changeset
165 test_sacurineTest_oplsda <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
166
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ethevenot
parents:
diff changeset
167 testDirC <- "sacurineTest"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
168 argLs <- list(respC = "gender",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
169 predI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
170 orthoI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
171 testL = "TRUE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
172
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ethevenot
parents:
diff changeset
173 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
174 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
175
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ethevenot
parents:
diff changeset
176 checkEquals(outLs[["samDF"]][181, "gender_OPLSDA_predictions"], "F")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
177
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ethevenot
parents:
diff changeset
178 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
179
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ethevenot
parents:
diff changeset
180 test_sacurine_oplsAge <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
181
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ethevenot
parents:
diff changeset
182 testDirC <- "sacurine"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
183 argLs <- list(respC = "age",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
184 predI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
185 orthoI = "1",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
186 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
187
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
188 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
189 outLs <- wrapperCallF(argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
190
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
191 checkEqualsNumeric(outLs[["varDF"]][1, "age_OPLS_VIP_ortho"], 0.3514378, tolerance = 1e-7)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
192 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
193
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
194 test_example1_plsda <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
195
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ethevenot
parents:
diff changeset
196 testDirC <- "example1"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
197 argLs <- list(respC = "traitment",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
198 predI = "3",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
199 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
200 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
201
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
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 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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206
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ethevenot
parents:
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207 test_example2_pca <- function() {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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208
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ethevenot
parents:
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209 testDirC <- "example2"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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210 argLs <- list(respC = "none",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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211 predI = "NA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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212 orthoI = "0",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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213 testL = "FALSE")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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214
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ethevenot
parents:
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215 argLs <- c(defaultArgF(testDirC), argLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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 }