annotate univariate_script.R @ 2:09799fc16bc6 draft

planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents ef64d3752050
children 140290de7986
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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1 univariateF <- function(datMN,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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2 samDF,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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3 varDF,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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4 facC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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5 tesC = c("ttest", "wilcoxon", "anova", "kruskal", "pearson", "spearman")[1],
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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6 adjC = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")[7],
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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7 thrN = 0.05) {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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8
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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9
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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10 ## Option
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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11 ##---------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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12
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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13 strAsFacL <- options()$stringsAsFactors
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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14 options(stingsAsFactors = FALSE)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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15 options(warn = -1)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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16
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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17 if(mode(samDF[, facC]) == "character") {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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18 facFcVn <- factor(samDF[, facC])
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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19 facLevVc <- levels(facFcVn)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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20 } else
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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21 facFcVn <- samDF[, facC]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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22
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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23 cat("\nPerforming '", tesC, "'\n", sep="")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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24
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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25 varPfxC <- paste0(make.names(facC), "_", tesC, "_")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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26
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27 if(tesC %in% c("ttest", "wilcoxon", "pearson", "spearman")) {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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28
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29 switch(tesC,
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30 ttest = {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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31 staF <- function(y) diff(tapply(y, facFcVn, function(x) mean(x, na.rm = TRUE)))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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32 tesF <- function(y) t.test(y ~ facFcVn)[["p.value"]]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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33 },
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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34 wilcoxon = {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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35 staF <- function(y) diff(tapply(y, facFcVn, function(x) median(x, na.rm = TRUE)))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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36 tesF <- function(y) wilcox.test(y ~ facFcVn)[["p.value"]]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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37 },
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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38 pearson = {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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39 staF <- function(y) cor(facFcVn, y, method = "pearson", use = "pairwise.complete.obs")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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40 tesF <- function(y) cor.test(facFcVn, y, method = "pearson", use = "pairwise.complete.obs")[["p.value"]]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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41 },
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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42 spearman = {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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43 staF <- function(y) cor(facFcVn, y, method = "spearman", use = "pairwise.complete.obs")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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44 tesF <- function(y) cor.test(facFcVn, y, method = "spearman", use = "pairwise.complete.obs")[["p.value"]]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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45 })
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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46
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47 staVn <- apply(datMN, 2, staF)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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48
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49 fdrVn <- p.adjust(apply(datMN,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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50 2,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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51 tesF),
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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52 method = adjC)
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53
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54 sigVn <- as.numeric(fdrVn < thrN)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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55
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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56 if(tesC %in% c("ttest", "wilcoxon"))
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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57 varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "."), "_")
0
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58
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59 varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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60
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61 varDF[, paste0(varPfxC, adjC)] <- fdrVn
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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62
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63 varDF[, paste0(varPfxC, "sig")] <- sigVn
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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64
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65 } else if(tesC == "anova") {
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66
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67 ## getting the names of the pairwise comparisons 'class1Vclass2'
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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68 prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]])
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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69
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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70 prwVc <- gsub("-", ".", prwVc, fixed = TRUE) ## 2016-08-05: '-' character in dataframe column names seems not to be converted to "." by write.table on ubuntu R-3.3.1
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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71
0
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72 aovMN <- t(apply(datMN, 2, function(varVn) {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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73
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74 aovMod <- aov(varVn ~ facFcVn)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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75 pvaN <- summary(aovMod)[[1]][1, "Pr(>F)"]
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76 hsdMN <- TukeyHSD(aovMod)[["facFcVn"]]
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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77 c(pvaN, c(hsdMN[, c("diff", "p adj")]), as.numeric(hsdMN[, "p adj"] < thrN))
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78
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79 }))
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80
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81 aovMN[, 1] <- p.adjust(aovMN[, 1], method = adjC)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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82 sigVn <- as.numeric(aovMN[, 1] < thrN)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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83 aovMN <- cbind(aovMN[, 1], sigVn, aovMN[, 2:ncol(aovMN)])
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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84 ## aovMN[which(aovMN[, 2] < 1), (3 + length(prwVc)):ncol(aovMN)] <- NA
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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85 colnames(aovMN) <- paste0(varPfxC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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86 c(adjC,
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87 "sig",
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88 paste0(prwVc, "_dif"),
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89 paste0(prwVc, "_pva"),
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90 paste0(prwVc, "_sig")))
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91 aovMN[which(aovMN[, paste0(varPfxC, "sig")] < 1), paste0(varPfxC, c(paste0(prwVc, "_pva"), paste0(prwVc, "_sig")))] <- NA
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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92
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93 varDF <- cbind.data.frame(varDF, as.data.frame(aovMN))
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94
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95 } else if(tesC == "kruskal") {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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96
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97 ## getting the names of the pairwise comparisons 'class1Vclass2'
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98 nemMN <- posthoc.kruskal.nemenyi.test(datMN[, 1], facFcVn, "Tukey")[["p.value"]]
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99 nemVl <- c(lower.tri(nemMN, diag = TRUE))
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100 nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl],
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101 colnames(nemMN)[c(col(nemMN))][nemVl])
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102 nemNamVc <- paste0(nemClaMC[, 1], ".", nemClaMC[, 2])
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103 nemNamVc <- paste0(varPfxC, nemNamVc)
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104
0
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105 nemMN <- t(apply(datMN, 2, function(varVn) {
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106
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107 pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]]
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108 varNemMN <- posthoc.kruskal.nemenyi.test(varVn, facFcVn, "Tukey")[["p.value"]]
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109 c(pvaN, c(varNemMN))
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110
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111 }))
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112 pvaVn <- nemMN[, 1]
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113 fdrVn <- p.adjust(pvaVn, method = adjC)
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114 sigVn <- as.numeric(fdrVn < thrN)
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115 nemMN <- nemMN[, c(FALSE, nemVl)]
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116 colnames(nemMN) <- paste0(nemNamVc, "_pva")
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117 nemSigMN <- nemMN < thrN
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118 mode(nemSigMN) <- "numeric"
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119 colnames(nemSigMN) <- paste0(nemNamVc, "_sig")
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120 nemMN[sigVn < 1, ] <- NA
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121 nemSigMN[sigVn < 1, ] <- NA
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122
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123 difMN <- sapply(1:nrow(nemClaMC), function(prwI) {
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124 prwVc <- nemClaMC[prwI, ]
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125 prwVi <- which(facFcVn %in% prwVc)
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126 prwFacFc <- factor(as.character(facFcVn)[prwVi], levels = prwVc)
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127 apply(datMN[prwVi, ], 2, function(varVn) -diff(as.numeric(tapply(varVn, prwFacFc, function(x) median(x, na.rm = TRUE)))))
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128 })
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129 colnames(difMN) <- gsub("_sig", "_dif", colnames(nemSigMN))
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130
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131 nemMN <- cbind(fdrVn, sigVn, difMN, nemMN, nemSigMN)
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132 colnames(nemMN)[1:2] <- paste0(varPfxC, c(adjC, "sig"))
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133
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134 varDF <- cbind.data.frame(varDF, as.data.frame(nemMN))
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135
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136 }
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137
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138 names(sigVn) <- rownames(varDF)
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139 sigSumN <- sum(sigVn, na.rm = TRUE)
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140 if(sigSumN) {
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141 cat("\nThe following ", sigSumN, " variable", ifelse(sigSumN > 1, "s", ""), " (", round(sigSumN / length(sigVn) * 100), "%) ", ifelse(sigSumN > 1, "were", "was"), " found significant at the ", thrN, " level:\n", sep = "")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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142 cat(paste(rownames(varDF)[sigVn > 0], collapse = "\n"), "\n", sep = "")
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143 } else
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144 cat("\nNo significant variable found at the selected ", thrN, " level\n", sep = "")
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145
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146 options(stingsAsFactors = strAsFacL)
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147
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148 return(varDF)
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149
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150 }