R/meanTech.R

In rtpcr: qPCR Data Analysis

#' @title Computing the mean of technical replicates
#'
#' @description
#' Computes the arithmetic mean of technical replicates for each sample or group.
#' This is often performed before ANOVA or other statistical analyses to simplify
#' comparisons between experimental groups.
#'
#' @details
#' The \code{meanTech} function calculates the mean of technical replicates
#' based on one or more grouping columns. This reduces the dataset to a single
#' representative value per group, facilitating downstream analysis such as
#' fold change calculation or ANOVA.
#'
#' @author
#' Ghader Mirzaghaderi
#'
#' @export
#'
#' @import tidyr
#' @import dplyr
#' @import reshape2
#'
#' @param x A raw data frame containing technical replicates.
#' @param numOfFactors Integer. Number of experimental factor columns
#' @param block Character. Block column name or \code{NULL}. 
#'
#' @param groups
#' An integer vector or character vector specifying the column(s) to group
#' by before calculating the mean of technical replicates.
#' 
#' @param set_missing_target_Ct_to_40 If \code{TRUE}, missing target gene Ct values become 40; if \code{FALSE} (default), they become NA. 
#' @param numberOfrefGenes Integer. Number of reference genes.
#'
#' @return
#' A data frame with the mean of technical replicates for each group.
#'
#' @examples
#'
#' # Example input data frame with technical replicates
#' data1 <- read.csv(system.file("extdata", "data_withTechRep.csv", package = "rtpcr"))
#'
#' # Calculate mean of technical replicates using first four columns as groups
#' meanTech(data1,
#'          groups = 1:2,
#'          numOfFactors = 1,
#'          numberOfrefGenes = 1,
#'          block = NULL)
#' 
#' # Another example using different dataset and grouping columns
#' data2 <- read.csv(system.file("extdata", "data_Lee_etal2020qPCR.csv", package = "rtpcr"))
#' meanTech(data2, groups = 1:3,
#'          numOfFactors = 2,
#'          numberOfrefGenes = 1,
#'          block = NULL)


meanTech <- function(x, groups, numOfFactors, numberOfrefGenes, block,
                     set_missing_target_Ct_to_40 = FALSE){

  x <- .cleanup(x = x, numOfFactors = numOfFactors + 1, numberOfrefGenes = numberOfrefGenes, block = block,
                set_missing_target_Ct_to_40 = set_missing_target_Ct_to_40)
  
  g <- colnames(x)[groups]

  # Concatenate the columns using paste0
  x$T <- do.call(paste, c(x[groups], sep = ":"))

  data_meanBiolRep <- x %>%
    group_by(across(all_of(g))) %>%
    summarise(across(where(is.numeric), mean, na.rm = TRUE))

  y <- data_meanBiolRep
  m <- ncol(y)-4
  databiol <- y[,-m]
  return(as.data.frame(databiol))
}