Nothing
"oncotree.fit" <-
function(dataset, error.fun=function(x,y){sum((x-y)^2)}){
cur.matrix <- formatData(dataset)
parent <- build.parent(cur.matrix)
# plotinfo <- build.plot(parent)
estimate.error.rates <- function(otree, error.fun){
mse <- function(eps, observed){
err <- try({error.rates(otree) <- eps}, silent=TRUE)
if (is.character(err)) return(otree$nmut)
md.eps <- marginal.distr(otree, with.errors=TRUE)
error.fun(observed[-1],md.eps[-1])
}
obs <- colMeans(otree$data)
min.p <- min(marginal.distr(otree, with.errors=FALSE))
res <- optim(c(0,0), mse, method="L-BFGS-B", lower=c(0,0), upper=c(min.p-0.001, 1-min.p), observed=obs)
res$par
}
otree <- list(data=cur.matrix, nmut=ncol(cur.matrix), parent=parent)
# ,level=plotinfo$level, numchild=plotinfo$numchild,
# levelnodes=plotinfo$levelnodes, levelgrp=plotinfo$levelgrp)
if (!is.null(error.fun)){
eps.hat <- estimate.error.rates(otree, error.fun=error.fun)
error.rates(otree) <- eps.hat
}
class(otree)<-"oncotree"
return(otree)
}
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