Mercurial > repos > melpetera > batchcorrection

annotate runit/batchcorrection_tests.R @ 0:71d83d8920bf draft

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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
author melpetera
date Tue, 09 Aug 2016 06:47:41 -0400
parents
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
parents:
diff changeset
1 test_input_allLoessPool <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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3 testDirC <- "input"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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4 determineL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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5 allLoessL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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6 argLs <- list(method = "all_loess_pool",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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7 span = "1")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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9 if(!allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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10 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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12 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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13 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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15 checkEqualsNumeric(outLs[['datMN']][1, 1], 25803076, tolerance = 1e-3)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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17 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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19 test_input_allLoessSample <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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21 testDirC <- "input"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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22 determineL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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23 allLoessL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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24 argLs <- list(method = "all_loess_sample",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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25 span = "1")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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27 if(!allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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28 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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30 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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31 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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33 checkEqualsNumeric(outLs[['datMN']][1, 1], 23402048, tolerance = 1e-3)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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35 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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37 test_example1_allLoessSample <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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39 testDirC <- "example1"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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40 determineL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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41 allLoessL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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42 argLs <- list(method = "all_loess_sample",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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43 span = "1")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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45 if(!allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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46 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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48 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
melpetera
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49 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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51 checkEqualsNumeric(outLs[['datMN']][1, 1], 21732604, tolerance = 1e-3)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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53 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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55 test_example1_allLoessSampleSpan06 <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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57 testDirC <- "example1"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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58 determineL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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59 allLoessL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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60 argLs <- list(method = "all_loess_sample",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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61 span = "0.6")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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63 if(!allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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64 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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66 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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67 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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69 checkEqualsNumeric(outLs[['datMN']][1, 1], 134619170, tolerance = 1e-3)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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73 test_sacurine_allLoessPool <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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75 testDirC <- "sacurine"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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76 determineL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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77 allLoessL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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78 argLs <- list(method = "all_loess_pool",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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79 span = "1")
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81 if(!allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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82 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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84 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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85 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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87 checkEqualsNumeric(outLs[['datMN']]["HU_neg_017", "M53T345"], 7902.366, tolerance = 1e-3)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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90 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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92 test_sacurine_determinebc <- function() {
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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94 testDirC <- "sacurine"
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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95 determineL <- TRUE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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96 allLoessL <- FALSE
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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97 argLs <- list(ref_factor = "batch",
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98 span = "none")
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99
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100 if(!allLoessL)
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101 argLs[["analyse"]] <- ifelse(determineL, "determine_bc", "batch_correction")
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102
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103 argLs <- c(defaultArgF(testDirC, determineL = determineL), argLs)
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104 outLs <- wrapperCallF(argLs, allLoessL = allLoessL)
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105
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106 checkEqualsNumeric(outLs[['sumDF']]["M59T62", "batch.2.linear"], 3, tolerance = 1e-3)
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107
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108
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109 }