Nothing
"summary.swap"<-
function(object, method=NULL, ncoef=length(object$alt.coef),nloc=object$nloc,...)
{
### summarize a swap.cycle object
this.call <- sys.call()
if (exists("unique.default")) unique <- unique.default
if (missing(method))
method <-
if(diff(dim(object$config))[1] < 0 )
"F2"
else
"BC1" #includes RIL cases
if(method=="F2") {
if (is.null(ncoef)) ncoef <- ((max(object$config) - 1) %/% 2 + 1) * 2
if (is.null(nloc)) nloc <- ncoef/ 2
}
else
{
if (is.null(ncoef)) {
if (is.null(nloc))
ncoef <- nloc <- max(object$config)
else
ncoef <- nloc
}
else
nloc <- ncoef
}
coefs <- rep(0, ncoef)
rep.post <- rep(object$post, rep(nrow(object$coefs), length(object$post
)))
cp <- object$coefs * rep.post
tap.coef <- tapply(cp, object$conf, sum)
coefs[sort(unique(c( object$config )))] <- if (method=="F2") tap.coef[-1] else tap.coef
coefs <- coefs/sum(object$post)
if (method=="F2") {
locs <- apply((object$config - 1) %/% 2 + 1, 2:3, function(x) {unique(c( x[x > 0]) )})
}
else
locs <- object$config
diml <- dim(locs)
if(length(diml) == 2)
diml <- c(1, diml)
loc.post <- rep(0, nloc)
rep.marg <- rep(object$marg, rep(diml[1], diml[2] * diml[3]))
loc.post[sort(unique(c( locs )))] <-
tapply(rep.marg, locs, sum)/sum(rep.marg)*diml[2]
## note assumption that second subscript tells size of model
blk.ratio <- apply(object$cond/object$marg, 2, mean)
res <- list(loc.posterior = loc.post, coefs = coefs,
ratio = list(mean = mean(blk.ratio),
var = var(blk.ratio)/length(blk.ratio)),
setup=c(genes=diml[2],nreps=diml[3],nloc=nloc)
,call=this.call)
class(res) <- "summary.swap"
res
}
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