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annotate runit/univariate_tests.R @ 2:09799fc16bc6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents
children 140290de7986
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
1 test_input_kruskal <- function() {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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3 testDirC <- "input"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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4 argLs <- list(facC = "ageGroup",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
5 tesC = "kruskal",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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6 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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7 thrN = "0.05")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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8
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
9 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
10 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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12 checkEqualsNumeric(outLs[["varDF"]]["HMDB01032", "ageGroup_kruskal_senior.experienced_pva"], 0.1231246, tolerance = 1e-6)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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13
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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14 }
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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16 test_example1_wilcoxDif <- function() {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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17
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
18 testDirC <- "example1"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
19 argLs <- list(facC = "jour",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
20 tesC = "wilcoxon",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
21 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
22 thrN = "0.05")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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23
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
24 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
25 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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26
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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27 checkEqualsNumeric(outLs[["varDF"]]["MT3", "jour_wilcoxon_J3.J10_dif"], 0.216480042, tolerance = 1e-8)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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29 }
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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30
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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31 test_example1_ttestFdr <- function() {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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32
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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33 testDirC <- "example1"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
34 argLs <- list(facC = "jour",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
35 tesC = "ttest",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
36 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
37 thrN = "0.05")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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38
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
39 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
40 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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41
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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42 checkEqualsNumeric(outLs[["varDF"]]["MT3", "jour_ttest_J3.J10_fdr"], 0.7605966, tolerance = 1e-6)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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44 }