R/totSS.R

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

#' Calculating Total Sum of Squares (TSS)
#' @param X Mean centered and unit variance scaled matrix (see Details).
#' @return Total sum of squares.
#' @details Input matrix rows correspond to n observations and columns to m variables. For large matrices (here defined by m>3k), X is subsampled to speed up computation time. Currently, subsampling is achieved by selecting each selecting each third row element.
#' @author Torben Kimhofer \email{tkimhofer@@gmail.com}
#' @noRd
totSS <- function(X) {
    # to speed calculations up, sample X matrix if large enought nrow(X)<1000 |
    if (ncol(X) > 3000) {
        idx <- seq(from = 1, to = ncol(X), by = 3)
        tss <- sum(apply(X[, idx], 1, function(x) {
            crossprod(x)
        }))
    } else {
        tss <- sum(apply(X, 1, function(x) {
            crossprod(x)
        }))
    }
    return(tss)
}