Mercurial > repos > ethevenot > batchcorrection

annotate runit/batchcorrection_tests.R @ 0:b74d1d533dea draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author ethevenot
date Thu, 04 Aug 2016 11:40:35 -0400
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
diff changeset
1 test_input_allLoessPool <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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3 testDirC <- "input"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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4 determineL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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5 allLoessL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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6 argLs <- list(method = "all_loess_pool",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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7 span = "1")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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9 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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10 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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12 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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13 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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15 checkEqualsNumeric(outLs[['datMN']][1, 1], 25803076, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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17 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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19 test_input_allLoessSample <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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21 testDirC <- "input"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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22 determineL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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23 allLoessL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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24 argLs <- list(method = "all_loess_sample",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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25 span = "1")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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27 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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28 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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30 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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31 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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33 checkEqualsNumeric(outLs[['datMN']][1, 1], 23402048, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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35 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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37 test_example1_allLoessSample <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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39 testDirC <- "example1"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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40 determineL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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41 allLoessL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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42 argLs <- list(method = "all_loess_sample",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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43 span = "1")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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45 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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46 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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48 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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49 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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51 checkEqualsNumeric(outLs[['datMN']][1, 1], 21732604, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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53 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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55 test_example1_allLoessSampleSpan06 <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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57 testDirC <- "example1"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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58 determineL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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59 allLoessL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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60 argLs <- list(method = "all_loess_sample",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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61 span = "0.6")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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63 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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64 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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66 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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67 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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69 checkEqualsNumeric(outLs[['datMN']][1, 1], 134619170, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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71 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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73 test_sacurine_allLoessPool <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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75 testDirC <- "sacurine"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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76 determineL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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77 allLoessL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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78 argLs <- list(method = "all_loess_pool",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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79 span = "1")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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81 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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82 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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84 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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85 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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87 checkEqualsNumeric(outLs[['datMN']]["HU_neg_017", "M53T345"], 7902.366, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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90 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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92 test_sacurine_determinebc <- function() {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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94 testDirC <- "sacurine"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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95 determineL <- TRUE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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96 allLoessL <- FALSE
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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97 argLs <- list(ref_factor = "batch",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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98 span = "none")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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99
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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100 if(!allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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101 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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102
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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103 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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104 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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parents:
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105
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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106 checkEqualsNumeric(outLs[['sumDF']]["M59T62", "batch.2.linear"], 3, tolerance = 1e-3)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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107
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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108
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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109 }