R/classCNV.R

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

classCNV <- function(x, mixture, threshold.CNV.0, 
        threshold.CNV.k) {
        mm <- mixture$parameter$mu
        ss <- mixture$parameter$sigma
        pp <- mixture$parameter$pi
        k <- length(ss)
        ans <- matrix(NA, nrow = length(x), ncol = k)
        for (i in seq_len(k)) ans[, i] <- pp[i] * dnorm(x, 
            mm[i], ss[i])
        if (any(x <= threshold.CNV.0)) {
            k <- k + 1
            ans <- cbind(ifelse(x <= threshold.CNV.0, 
                Inf, 0), ans)
        }
        if (any(x >= threshold.CNV.k)) {
            k <- k + 1
            ans <- cbind(ans, ifelse(x >= threshold.CNV.k, 
                Inf, 0))
        }
        out <- apply(ans, 1, function(x) which.max(x)[1])
        probs <- ans/rowSums(ans)
        probs[is.na(probs)] <- 1
        attr(out, "probabilities") <- probs
        attr(out, "k") <- k
        out
}