R/analyzeExperiments.R

In dosorio/ccCINTROP: Calculate and plot the CC50

#' @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)
}