R/anova.CNVassoc.R

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

anova.CNVassoc <- function(object, ...) {
        
        if (length(list(object, ...)) <= 1L) 
            stop("anova requires two nested models")
        objects <- list(object, ...)
        
        responses <- as.character(lapply(objects, 
            function(x) deparse(x$terms[[2L]])))
        
        sameresp <- responses == responses[1L]
        
        if (!all(sameresp)) {
            stop("models might have the same response ")
        }
        
        ns <- vapply(objects, function(x) length(x$y), 0)
        if (any(ns != ns[1L])) 
            stop("models were not all fitted to the same size of dataset")
        
        mod1 <- objects[[1]]
        mod2 <- objects[[2]]
        chi <- 2 * (logLik(mod1)[1] - logLik(mod2)[1])
        chi <- as.double(abs(chi))
        df <- logLik(mod1)[2] - logLik(mod2)[2]
        df <- as.integer(abs(df))
        pvalue <- pchisq(abs(chi), abs(df), lower.tail = FALSE)
        
        out <- c(chi = chi, df = df, pvalue = pvalue)
        
        out <- list(chi.test = out, mod1 = mod1, 
            mod2 = mod2)
        
        class(out) <- "anova.CNVassoc"
        
        out
        
}