Mercurial > repos > ethevenot > univariate
diff 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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--- a/univariate_script.R Sat Jul 30 12:38:02 2016 -0400 +++ b/univariate_script.R Sat Aug 06 12:42:42 2016 -0400 @@ -54,7 +54,7 @@ sigVn <- as.numeric(fdrVn < thrN) if(tesC %in% c("ttest", "wilcoxon")) - varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "-"), "_") + varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "."), "_") varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn @@ -67,6 +67,8 @@ ## getting the names of the pairwise comparisons 'class1Vclass2' prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]]) + 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 + aovMN <- t(apply(datMN, 2, function(varVn) { aovMod <- aov(varVn ~ facFcVn) @@ -97,9 +99,9 @@ nemVl <- c(lower.tri(nemMN, diag = TRUE)) nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl], colnames(nemMN)[c(col(nemMN))][nemVl]) - nemNamVc <- paste0(nemClaMC[, 1], "-", nemClaMC[, 2]) + nemNamVc <- paste0(nemClaMC[, 1], ".", nemClaMC[, 2]) nemNamVc <- paste0(varPfxC, nemNamVc) - + nemMN <- t(apply(datMN, 2, function(varVn) { pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]]