Mercurial > repos > ethevenot > univariate

annotate runit/univariate_tests.R @ 3:140290de7986 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
author ethevenot
date Sun, 30 Oct 2016 14:17:09 -0400
parents 09799fc16bc6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
1 test_input_anova <- function() {
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
3 testDirC <- "input"
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
4 argLs <- list(facC = "qual",
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
5 tesC = "anova",
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
6 adjC = "fdr",
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
7 thrN = "0.05")
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
9 argLs <- c(defaultArgF(testDirC), argLs)
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
10 outLs <- wrapperCallF(argLs)
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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12 checkEqualsNumeric(outLs[["varDF"]]["v6", "qual_anova_fdr"], 1.924156e-03, tolerance = 1e-6)
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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14 checkEqualsNumeric(outLs[["varDF"]]["v4", "qual_anova_D.C_fdr"], 0.01102016, tolerance = 1e-6)
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
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16 }
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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18 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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20 testDirC <- "input"
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
21 argLs <- list(facC = "qual",
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
22 tesC = "kruskal",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
23 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
24 thrN = "0.05")
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:
diff changeset
26 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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27 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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29 checkEqualsNumeric(outLs[["varDF"]]["v4", "qual_kruskal_fdr"], 0.0008194662, tolerance = 1e-7)
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
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140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
ethevenot
parents: 2
diff changeset
31 checkEqualsNumeric(outLs[["varDF"]]["v6", "qual_kruskal_D.A_fdr"], 0.002945952, tolerance = 1e-7)
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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parents:
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33 }
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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35 test_example1_wilcoxDif <- function() {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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parents:
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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37 testDirC <- "example1"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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38 argLs <- list(facC = "jour",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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39 tesC = "wilcoxon",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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40 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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41 thrN = "0.05")
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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43 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
diff changeset
44 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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46 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
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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48 }
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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50 test_example1_ttestFdr <- function() {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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52 testDirC <- "example1"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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53 argLs <- list(facC = "jour",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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54 tesC = "ttest",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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55 adjC = "fdr",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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56 thrN = "0.05")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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58 argLs <- c(defaultArgF(testDirC), argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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59 outLs <- wrapperCallF(argLs)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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61 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
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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63 }