Mercurial > repos > ethevenot > biosigner

annotate tests/biosigner_tests.R @ 0:48e4be935243 draft

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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
author ethevenot
date Wed, 27 Jul 2016 11:40:20 -0400
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48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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1 library(RUnit)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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3 wrapperF <- function(argVc) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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6 #### Start_of_testing_code <- function() {}
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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9 ##------------------------------
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10 ## Initializing
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11 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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13 ## options
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14 ##--------
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16 strAsFacL <- options()$stringsAsFactors
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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17 options(stringsAsFactors = FALSE)
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19 ## libraries
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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20 ##----------
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22 suppressMessages(library(biosigner))
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24 if(packageVersion("biosigner") < "1.0.0")
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25 stop("Please use 'biosigner' versions of 1.0.0 and above")
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26 if(packageVersion("ropls") < "1.4.0")
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27 stop("Please use 'ropls' versions of 1.4.0 and above")
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29 ## constants
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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30 ##----------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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32 modNamC <- "Biosigner" ## module name
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34 topEnvC <- environment()
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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35 flgC <- "\n"
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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37 ## functions
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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38 ##----------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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40 flgF <- function(tesC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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41 envC = topEnvC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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42 txtC = NA) { ## management of warning and error messages
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44 tesL <- eval(parse(text = tesC), envir = envC)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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46 if(!tesL) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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48 sink(NULL)
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49 stpTxtC <- ifelse(is.na(txtC),
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50 paste0(tesC, " is FALSE"),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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51 txtC)
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53 stop(stpTxtC,
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54 call. = FALSE)
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56 }
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58 } ## flgF
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61 ## log file
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62 ##---------
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63
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64 sink(argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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65
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66 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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67 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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68
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69
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70 ## arguments
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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71 ##----------
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72
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73 xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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74 check.names = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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75 header = TRUE,
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76 row.names = 1,
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77 sep = "\t")))
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78
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79 samDF <- read.table(argVc["sampleMetadata_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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80 check.names = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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81 header = TRUE,
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82 row.names = 1,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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83 sep = "\t")
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84 flgF("identical(rownames(xMN), rownames(samDF))", txtC = "Sample names (or number) in the data matrix (first row) and sample metadata (first column) are not identical; use the 'Check Format' module in the 'Quality Control' section")
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85
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86 varDF <- read.table(argVc["variableMetadata_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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87 check.names = FALSE,
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88 header = TRUE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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89 row.names = 1,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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90 sep = "\t")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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91 flgF("identical(colnames(xMN), rownames(varDF))", txtC = "Variable names (or number) in the data matrix (first column) and sample metadata (first column) are not identical; use the 'Check Format' module in the 'Quality Control' section")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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92
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93 flgF("argVc['respC'] %in% colnames(samDF)",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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94 txtC = paste0("Class argument (", argVc['respC'], ") must be either none or one of the column names (first row) of your sample metadata"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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95 respVc <- samDF[, argVc["respC"]]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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96 flgF("mode(respVc) == 'character'",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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97 txtC = paste0("'", argVc['respC'], "' column of sampleMetadata does not contain only characters"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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98 respFc <- factor(respVc)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
99 flgF("length(levels(respFc)) == 2",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
100 txtC = paste0("'", argVc['respC'], "' column of sampleMetadata does not contain only 2 types of characters (e.g., 'case' and 'control')"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
101 tierMaxC <- ifelse("tierC" %in% names(argVc), argVc["tierC"], "S")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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102 pvalN <- ifelse("pvalN" %in% names(argVc), as.numeric(argVc["pvalN"]), 0.05)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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103
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104
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parents:
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105 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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106 ## Computation and plot
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parents:
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107 ##------------------------------
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108
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109
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parents:
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110 sink()
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111
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parents:
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112 optWrnN <- options()$warn
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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113 options(warn = -1)
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114
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115 if("seedI" %in% names(argVc) && argVc["seedI"] != "0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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116 set.seed(as.integer(argVc["seedI"]))
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117
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parents:
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118 bsnLs <- biosign(x = xMN,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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119 y = respFc,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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120 methodVc = ifelse("methodC" %in% names(argVc), argVc["methodC"], "all"),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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121 bootI = ifelse("bootI" %in% names(argVc), as.numeric(argVc["bootI"]), 50),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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122 pvalN = pvalN,
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parents:
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123 printL = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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124 plotL = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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125 .sinkC = argVc["information"])
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126
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parents:
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127 if("seedI" %in% names(argVc) && argVc["seedI"] != "0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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128 set.seed(NULL)
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129
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parents:
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130 tierMC <- bsnLs@tierMC
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131
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parents:
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132 if(!is.null(tierMC)) {
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ethevenot
parents:
diff changeset
133 plot(bsnLs,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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134 tierMaxC = tierMaxC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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135 file.pdfC = argVc["figure_tier"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
136 .sinkC = argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
137 plot(bsnLs,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
138 tierMaxC = tierMaxC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
139 typeC = "boxplot",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
140 file.pdfC = argVc["figure_boxplot"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
141 .sinkC = argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
142 } else {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
143 pdf(argVc["figure_tier"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
144 plot(1, bty = "n", type = "n",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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145 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
146 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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147 labels = "No significant variable to display")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
148 dev.off()
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parents:
diff changeset
149 pdf(argVc["figure_boxplot"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
150 plot(1, bty = "n", type = "n",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
151 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
152 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
diff changeset
153 labels = "No significant variable to display")
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ethevenot
parents:
diff changeset
154 dev.off()
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parents:
diff changeset
155 }
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parents:
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156
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parents:
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157
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parents:
diff changeset
158 options(warn = optWrnN)
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parents:
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159
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parents:
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160
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parents:
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161 ##------------------------------
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parents:
diff changeset
162 ## Print
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ethevenot
parents:
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163 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
diff changeset
164
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ethevenot
parents:
diff changeset
165 sink(argVc["information"], append = TRUE)
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parents:
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166
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ethevenot
parents:
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167 tierFullVc <- c("S", LETTERS[1:5])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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168 tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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169
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ethevenot
parents:
diff changeset
170 if(sum(tierMC %in% tierVc)) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
171 cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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172 print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
173 drop = FALSE])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
174 cat("\nAccuracy:\n")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
175 print(round(getAccuracyMN(bsnLs), 3))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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176 } else
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ethevenot
parents:
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177 cat("\nNo significant variable found for any classifier\n")
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parents:
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178
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179
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parents:
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180 ##------------------------------
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parents:
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181 ## Ending
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parents:
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182 ##------------------------------
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parents:
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183
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parents:
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184 ## Saving
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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185 ##-------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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186
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ethevenot
parents:
diff changeset
187 if(!is.null(tierMC)) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
188 tierDF <- data.frame(tier = sapply(rownames(varDF),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
189 function(varC) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
190 varTirVc <- tierMC[varC, ]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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191 varTirVc <- names(varTirVc)[varTirVc %in% tierVc]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
192 paste(varTirVc, collapse = "|")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
193 }),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
194 stringsAsFactors = FALSE)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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195 colnames(tierDF) <- paste(argVc["respC"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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196 colnames(tierDF),
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197 paste(tierVc, collapse = ""),
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198 sep = "_")
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199 varDF <- cbind.data.frame(varDF, tierDF)
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200 }
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201
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202 ## variableMetadata
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203
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204 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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205 varDF)
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206 write.table(varDF,
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207 file = argVc["variableMetadata_out"],
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208 quote = FALSE,
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209 row.names = FALSE,
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210 sep = "\t")
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211
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212
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213 ## Closing
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214 ##--------
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215
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216 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
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217 as.character(Sys.time()), "\n", sep = "")
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218
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219 sink()
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220
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221 options(stringsAsFactors = strAsFacL)
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222
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223
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224 #### End_of_testing_code <- function() {}
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225
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226
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227 return(list(bsnLs = bsnLs))
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228
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229
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230 rm(list = ls())
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231
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232
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233 }
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234
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235
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236 exaDirOutC <- "output"
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237 if(!file.exists(exaDirOutC))
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238 stop("Please create an 'output' subfolder into the (current) 'tests' folder")
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239
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240 tesArgLs <- list(sacurine_all = c(respC = "gender",
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241 methodC = "all",
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242 bootI = "5",
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243 pvalN = "0.05",
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244 seedI = "123",
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245 .chkC = "checkEqualsNumeric(getAccuracyMN(outLs[['bsnLs']])['AS', 'randomforest'], 0.8534348, tolerance = 1e-7)"))
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246
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247 for(tesC in names(tesArgLs))
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248 tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
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249 dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
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250 sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"),
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251 variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"),
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252 variableMetadata_out = file.path(exaDirOutC, "variableMetadata.tsv"),
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253 figure_tier = file.path(exaDirOutC, "figure-tier.pdf"),
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254 figure_boxplot = file.path(exaDirOutC, "figure-boxplot.pdf"),
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255 information = file.path(exaDirOutC, "information.txt"))
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256
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257 for(tesC in names(tesArgLs)) {
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258 print(tesC)
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259 outLs <- wrapperF(tesArgLs[[tesC]])
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260 if(".chkC" %in% names(tesArgLs[[tesC]]))
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261 stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))
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262 }
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263
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264 message("Checks successfully completed")