#' @export analyzeExperiments
analyzeExperiments <- function(file){
data <- read.table(file,header = TRUE,row.names = 1)
temp <- tempdir()
write.table(t(data),row.names = FALSE,file = paste0(temp,"temp.out"))
data <- stack(read.table(paste0(temp,"temp.out"),header = TRUE))
anova <- TukeyHSD(aov(formula = values~ind,data = data),conf.level = 0.95)
anova$ind <- as.data.frame.array(anova$ind)
anova$ind[,4] <- p.adjust(anova$ind[,4],method = "bonferroni")
anova$ind[,5] <- rep("",dim(anova$ind)[1])
anova$ind[anova$ind[,4] < 0.1,5] <- "*"
anova$ind[anova$ind[,4] < 0.05,5] <- "**"
anova$ind[anova$ind[,4] < 0.01,5] <- "***"
anova <- anova$ind
anova <- anova[anova[,5] != "",]
dimnames(anova)[[2]] <- c("diff","lwr","upr","p","s")
message("Analysis: One-way ANOVA + Bonferroni correction")
return(anova)
}
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