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view runit/multivariate_tests.R @ 2:fa173e12e185 draft

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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
author ethevenot
date Sat, 06 Aug 2016 12:07:13 -0400
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test_input_pca <- function() {

    testDirC <- "input"
    argLs <- list(respC = "none",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_input_pcaGender <- function() {

    testDirC <- "input"
    argLs <- list(respC = "none",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE",
                  parMahalC = "gender")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_input_plsdaGender <- function() {

    testDirC <- "input"
    argLs <- list(respC = "gender",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")
    
    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_input_oplsAge <- function() {

    testDirC <- "input"
    argLs <- list(respC = "age",
                  predI = "1",
                  orthoI = "1",
                  testL = "FALSE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_input_oplsdaGender <- function() {

    testDirC <- "input"
    argLs <- list(respC = "gender",
                  predI = "1",
                  orthoI = "1",
                  testL = "FALSE")
    
    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_sacurine_pca <- function() {

    testDirC <- "sacurine"
    argLs <- list(respC = "none",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_sacurine_pcaGender <- function() {

    testDirC <- "sacurine"
    argLs <- list(respC = "none",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE",
                  parMahalC = "gender")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_sacurine_plsAge <- function() {

    testDirC <- "sacurine"
    argLs <- list(respC = "age",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")
    
    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_sacurine_plsdaGender <- function() {

    testDirC <- "sacurine"
    argLs <- list(respC = "gender",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_sacurineTest_pls <- function() {

    testDirC <- "sacurineTest"
    argLs <- list(respC = "age",
                  predI = "2",
                  orthoI = "0",
                  testL = "TRUE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)

    checkEqualsNumeric(outLs[["samDF"]][181, "age_PLS_predictions"], 40.82252, tolerance = 1e-5)
 
}

test_sacurineTest_opls <- function() {

    testDirC <- "sacurineTest"
    argLs <- list(respC = "age",
                  predI = "1",
                  orthoI = "2",
                  testL = "TRUE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)

    checkEqualsNumeric(outLs[["samDF"]][181, "age_OPLS_predictions"], 40.28963, tolerance = 1e-5)
 
}

test_sacurineTest_plsda <- function() {

    testDirC <- "sacurineTest"
    argLs <- list(respC = "gender",
                  predI = "2",
                  orthoI = "0",
                  testL = "TRUE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)

    checkEquals(outLs[["samDF"]][181, "gender_PLSDA_predictions"], "F")
 
}

test_sacurineTest_oplsda <- function() {

    testDirC <- "sacurineTest"
    argLs <- list(respC = "gender",
                  predI = "1",
                  orthoI = "1",
                  testL = "TRUE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)

    checkEquals(outLs[["samDF"]][181, "gender_OPLSDA_predictions"], "F")
 
}

test_sacurine_oplsAge <- function() {

    testDirC <- "sacurine"
    argLs <- list(respC = "age",
                  predI = "1",
                  orthoI = "1",
                  testL = "FALSE")

    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)

    checkEqualsNumeric(outLs[["varDF"]][1, "age_OPLS_VIP_ortho"], 0.3514378, tolerance = 1e-7)
}

test_example1_plsda <- function() {

    testDirC <- "example1"
    argLs <- list(respC = "traitment",
                  predI = "3",
                  orthoI = "0",
                  testL = "FALSE")
    
    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}

test_example2_pca <- function() {

    testDirC <- "example2"
    argLs <- list(respC = "none",
                  predI = "NA",
                  orthoI = "0",
                  testL = "FALSE")
    
    argLs <- c(defaultArgF(testDirC), argLs)
    outLs <- wrapperCallF(argLs)
 
}