Nothing
mixture <-
function (intensities, num.class, mix.method, threshold.0, threshold.k,
mu.ini, sigma.ini, pi.ini, var.equal)
{
method <- charmatch(mix.method, c("mixdist", "mclust", "EMmixt"))
miss.threshold0 <- missing(threshold.0)
miss.thresholdk <- missing(threshold.k)
if (!miss.threshold0 && threshold.0 > min(intensities))
num.class <- num.class - 1
else {
if (!miss.threshold0 && threshold.0 <= min(intensities))
warning("threshold.0 ignored because it's smaller than intensity minimum value")
threshold.0 <- -Inf
}
if (!miss.thresholdk && threshold.k < max(intensities))
num.class <- num.class - 1
else {
if (!miss.thresholdk && threshold.k >= max(intensities))
warning("threshold.k ignored because it's bigger than intensity maximum value")
threshold.k <- Inf
}
yy <- intensities[intensities > threshold.0 & intensities < threshold.k]
if (max(num.class) < 2) {
cc <- unique(c(-Inf, threshold.0, threshold.k, Inf))
out <- as.integer(cut(intensities, cc))
attr(out, "mixture") <- NULL
attr(out, "means") <- mean(yy)
attr(out, "sds") <- 0
attr(out, "probabilities") <- sapply(seq(along=unique(out)), function(j) ifelse(out==j,1,0))
num.class <- 1
}
else {
res <- mix(yy, method, num.class, mu.ini, sigma.ini, pi.ini, var.equal)
num.class <- res$G
out <- classCNV(intensities, res, threshold.0, threshold.k)
attr(out, "mixture") <- res
attr(out, "means") <- c(res$parameter$mu)
attr(out, "sds") <- c(res$parameter$sigma)
}
attr(out, "meanRatio") <- intensities
attr(out, "num.copies") <- c(1:num.class)
if (!miss.threshold0) {
attr(out, "means") <- c(min(intensities), attr(out, "means"))
attr(out, "sds") <- c(0, attr(out, "sds"))
attr(out, "num.copies") <- c(0, attr(out, "num.copies"))
}
if (!miss.thresholdk) {
attr(out, "means") <- c(attr(out, "means"), max(intensities))
attr(out, "sds") <- c(attr(out, "sds"), 0)
attr(out, "num.copies") <- c(attr(out, "num.copies"), num.class + 1)
}
out
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.