R/score.r

In yousefi138/dnamalci: Easy estimation of DNA methylation alcohol (DNAm-Alcs) scores

#' Calculate any of the DNA methylation alcohol scores from Liu et al. 2016
#'
#' @param x DNA methylation matrix (rows=CpG sites, columns=samples).
#' @param model Model name from available list (\code{\link{dnamalci.models}()}).
#' Default is the `dnamalc.144cpg` score. 
#' @return Scores derived for each sample in \code{x}.
#'
#' @export
dnamalci <- function(x, model = "dnamalc.144cpg") {
    stopifnot(is.matrix(x))

    ret <- dnamalci.get.model(model)
    ret$name <- model

    sites <- intersect(rownames(x), names(ret$coefficients))

    score <- rep(NA, ncol(x))
    if (length(sites) == 1)
        score <- ret$coefficients[sites] * x[sites,]
    if (length(sites) > 1)
        score <- as.vector(rbind(ret$coefficients[sites]) %*% x[sites,,drop=F])

    ret$sites <- sites
    ret$score <- score
    ret
}