R/rla.R

In rformassspectrometry/MsCoreUtils: Core Utils for Mass Spectrometry Data

#' @title Calculate relative log abundances
#'
#' @description
#'
#' `rla` calculates the relative log abundances (RLA, see reference) on a
#' `numeric` vector. `rowRla` performs row-wise RLA calculations on a numeric
#' `matrix`.
#'
#' @details
#'
#' The RLA is defined as the (log2) abundance of an analyte relative
#' to the median across all abundances of that analyte in samples of the
#' same group. The grouping of values can be defined with parameter `f`.
#'
#' @param x `numeric` (for `rla`) or `matrix` (for `rowRla`) with the
#'     abundances (in natural scale) on which the RLA should be calculated.
#'
#' @param f `factor`, `numeric` or `character` with the same length than `x`
#'     (or, for `rowRla` equal to the number of columns of `x`) allowing to
#'     define the grouping of values in `x`. If omitted all values are
#'     considered to be from the same group.
#'
#' @param transform `character(1)` defining the function to transform `x`.
#'     Defaults to `transform = "log2"` which `log2` transforms `x` prior to
#'     calculation. If `x` is already in log scale use `transform = "identity"`
#'     to avoid transformation of the values.
#'
#' @param na.rm `logical(1)` whether `NA` values should be removed prior to
#'     calculation of the group-wise medians.
#'
#' @return `numeric` with the relative log abundances (in log2 scale) with the
#'     same length than `x` (for `rla`) or `matrix` with the same dimensions
#'     than `x` (for `rowRla`).
#'
#' @rdname rla
#'
#' @author Johannes Rainer
#'
#' @export
#'
#' @references
#'
#' De Livera AM, Dias DA, De Souza D, Rupasinghe T, Pyke J, Tull D, Roessner U,
#' McConville M, Speed TP. Normalizing and integrating metabolomics data.
#' *Anal Chem* 2012 Dec 18;84(24):10768-76.
#'
#' @examples
#'
#' x <- c(3, 4, 5, 1, 2, 3, 7, 8, 9)
#'
#' grp <- c(1, 1, 1, 2, 2, 2, 3, 3, 3)
#'
#' rla(x, grp)
#'
#' x <- rbind(c(324, 4542, 3422, 3232, 5432, 6535, 3321, 1121),
#'      c(12, 3341, 3034, 6540, 34, 4532, 56, 1221))
#' grp <- c("a", "b", "b", "b", "a", "b", "a", "b")
#'
#' ## row-wise RLA values
#' rowRla(x, grp)
rla <- function(x, f = rep_len(1, length(x)),
                transform = c("log2", "log10", "identity"), na.rm = TRUE) {
    transform <- match.arg(transform)
    if (length(x) != length(f))
        stop("length of 'x' has to match length of 'f'", call. = FALSE)
    if (!is.factor(f))
        f <- factor(f, levels = unique(f))
    x <- do.call(transform, list(x))
    grp_meds <- unlist(lapply(split(x, f), median, na.rm = na.rm))
    res <- x - grp_meds[f]
    names(res) <- names(x)
    res
}

#' @rdname rla
#'
#' @export
rowRla <- function(x, f = rep_len(1, ncol(x)), transform = c("log2", "log10", "identity")) {
    res <- t(apply(x, MARGIN = 1, rla, f = f, transform = transform))
    dimnames(res) <- dimnames(x)
    res
}