R/getFC.R

In YonghuiDong/MSbox: Mass Spectrometry Tools

#' @title calculate fold change
#' @description calculate fold change among different samples.
#' @param x sample ion intensity matrix, row sample, column feature.
#' @param Group sample group information
#' @importFrom utils combn
#' @return a dataframe with mean values and fold changes
#' @export
#' @examples
#' dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
#' myGroup <- rep_len(LETTERS[1:2], 300)
#' ret <- getFC(dat, Group = myGroup)

 getFC <- function(x, Group = NULL){
    cat ("\n- Calculating Fold Changes...\n")
    #(1) check input
    Group <- as.factor(Group)
    if(is.null(Group)){stop("Please include group information")}
    if(length(levels(Group)) <= 1){stop("At least two sample groups should be included")}
    if(length(Group) != nrow(x)){stop("Missing group informaiton detected")}

    # calculate FC
    i <- split(1:nrow(x), Group)
    mean_int <- sapply(i, function(i){colMeans(x[i, ])})
    x <- t(mean_int)
    j <- combn(levels(Group), 2)
    f_change1 <- x[j[1,],] / x[j[2,],]
    f_change2 <- x[j[2,],] / x[j[1,],]
    ## remove NaN in f_change Matrix
    f_change <- rbind(f_change1, f_change2)
    f_change[is.nan(f_change)] <- 0
    rownames(f_change) <- c(paste0("Fold_", j[1,], "_vs_", j[2,]),
                           paste0("Fold_", j[2,], "_vs_", j[1,]))
    ret <- as.data.frame(t(f_change))
    return(round(ret, 2))
}