R/logLik.CNVassoc.R

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

logLik.CNVassoc <- function(object, ...) {
        x <- object
        family <- attr(x, "family")
        
        if (family == "binomial") {
            param <- matrix2vector(x$coefficients, 
                x$variant)
            ans <- logLike.logistic(param, x$y, 
                x$X, x$w, x$variant)
        }
        if (family == "poisson") {
            param <- matrix2vector(x$coefficients, 
                x$variant)
            ans <- logLike.poisson(param, x$y, 
                x$X, x$w, x$variant)
        }
        if (family == "gaussian") {
            param <- matrix2vector(x$coefficients, 
                x$variant)
            param <- c(param, x$sigma)
            ans <- logLike.norm(param, x$y, x$X, 
                x$w, x$variant)
        }
        if (family == "weibull") {
            param <- matrix2vector(x$coefficients, 
                x$variant)
            param <- c(param, x$alpha)
            ans <- logLike.weibull(param, x$y, 
                x$cens, x$X, x$w, x$variant)
        }
        df <- length(param)
        c(logLik = ans, df = df)
}