Mercurial > repos > ethevenot > univariate

comparison univariate_script.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 ef64d3752050
children 140290de7986
comparison
equal deleted inserted replaced
1:fdefbc780d2e 2:09799fc16bc6
52 method = adjC) 52 method = adjC)
53 53
54 sigVn <- as.numeric(fdrVn < thrN) 54 sigVn <- as.numeric(fdrVn < thrN)
55 55
56 if(tesC %in% c("ttest", "wilcoxon")) 56 if(tesC %in% c("ttest", "wilcoxon"))
57 varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "-"), "_") 57 varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "."), "_")
58 58
59 varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn 59 varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn
60 60
61 varDF[, paste0(varPfxC, adjC)] <- fdrVn 61 varDF[, paste0(varPfxC, adjC)] <- fdrVn
62 62
64 64
65 } else if(tesC == "anova") { 65 } else if(tesC == "anova") {
66 66
67 ## getting the names of the pairwise comparisons 'class1Vclass2' 67 ## getting the names of the pairwise comparisons 'class1Vclass2'
68 prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]]) 68 prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]])
69
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
69 71
70 aovMN <- t(apply(datMN, 2, function(varVn) { 72 aovMN <- t(apply(datMN, 2, function(varVn) {
71 73
72 aovMod <- aov(varVn ~ facFcVn) 74 aovMod <- aov(varVn ~ facFcVn)
73 pvaN <- summary(aovMod)[[1]][1, "Pr(>F)"] 75 pvaN <- summary(aovMod)[[1]][1, "Pr(>F)"]
95 ## getting the names of the pairwise comparisons 'class1Vclass2' 97 ## getting the names of the pairwise comparisons 'class1Vclass2'
96 nemMN <- posthoc.kruskal.nemenyi.test(datMN[, 1], facFcVn, "Tukey")[["p.value"]] 98 nemMN <- posthoc.kruskal.nemenyi.test(datMN[, 1], facFcVn, "Tukey")[["p.value"]]
97 nemVl <- c(lower.tri(nemMN, diag = TRUE)) 99 nemVl <- c(lower.tri(nemMN, diag = TRUE))
98 nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl], 100 nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl],
99 colnames(nemMN)[c(col(nemMN))][nemVl]) 101 colnames(nemMN)[c(col(nemMN))][nemVl])
100 nemNamVc <- paste0(nemClaMC[, 1], "-", nemClaMC[, 2]) 102 nemNamVc <- paste0(nemClaMC[, 1], ".", nemClaMC[, 2])
101 nemNamVc <- paste0(varPfxC, nemNamVc) 103 nemNamVc <- paste0(varPfxC, nemNamVc)
102 104
103 nemMN <- t(apply(datMN, 2, function(varVn) { 105 nemMN <- t(apply(datMN, 2, function(varVn) {
104 106
105 pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]] 107 pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]]
106 varNemMN <- posthoc.kruskal.nemenyi.test(varVn, facFcVn, "Tukey")[["p.value"]] 108 varNemMN <- posthoc.kruskal.nemenyi.test(varVn, facFcVn, "Tukey")[["p.value"]]
107 c(pvaN, c(varNemMN)) 109 c(pvaN, c(varNemMN))