R/totalArea.R

In kimsche/MetaboMate: All you need for NMR-based metabolic profiling with R!

#' Total area normalisation
#' @export
#' @aliases totalArea
#' @param X Input matrix where rows represent samples.
#' @param add.DilF Character string for new variable for dilution factor (will be exported as global environment variable). Can be left NULL if dilution factor should not be exported.
#' @author Torben Kimhofer \email{tkimhofer@@gmail.com}
totalArea <- function(X, add.DilF = "ta.dilf") {
    X[X == 0] <- 1e-04
    dil.F <- 1e+10/apply(X, 1, sum)
    X.ta <- t(apply(rbind(1:nrow(X)), 2, function(i) {
        X[i, ] * dil.F[i]
    }))
    if (!is.null(add.DilF)) {
        assign(add.DilF, dil.F, envir = .GlobalEnv)
    }
    return(X.ta)
}