Nothing
setMethod(f = "multiseg",signature = "CGHdata",
definition = function(.Object,CGHo,uniKmax=NULL,multiKmax=NULL){
uniKmax = getuniKmax(.Object,CGHo,uniKmax)
multiKmax = getmultiKmax(.Object,CGHo,uniKmax,multiKmax)
CGHr = new("CGHresults",CGHd=.Object,CGHo=CGHo)
from(CGHr) = "multiseg"
Res = list()
if ((CGHo["GCnorm"]=="linear") & (is.null(.Object@GCcontent))){
cat("[check multiseg] GCnorm can not be performed \n")
cat("[check multiseg] check that GCcontent is a record in the data\n")
stop()
}
if (CGHo["select"] != "none"){
if ( (CGHo["calling"]==FALSE) & (CGHo["wavenorm"]=="none") & (CGHo@GCnorm=="none")){
cat("[multiseg] multisegmean running \n")
Res = multisegmean(.Object,CGHo,uniKmax,multiKmax)
} else {
Kh = golden.search(.Object,CGHo,uniKmax,multiKmax)
multiKmax = Kh
eval(fun2run(CGHo))
}
} else {
eval(fun2run(CGHo))
}
cat("\n")
if ( (CGHo["wavenorm"]!="none") | (CGHo["GCnorm"]!="none") ){
theta(CGHr) = Res$theta
}
if (!is.null(.Object["genomic.position"])){
x = .Object["genomic.position"]
Res$mu = lapply(Res$mu,FUN = function(y){
y$begin = x[y$begin]
y$end = x[y$end]
return(y)
})
}
mu(CGHr) = Res$mu
loglik(CGHr) = list(multiloglik = Res$loglik)
nbiter(CGHr) = Res$nbiter
return(CGHr)
} # end function
)
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