\name{Clonality-internal}
\alias{calc.freq}
\alias{calculateLR}
\alias{class.all}
\alias{CM.pvalue}
\alias{complexts}
\alias{func}
\alias{GL}
\alias{grantLR}
\alias{indiv.test}
\alias{LRpv}
\alias{LRts}
\alias{oneseg}
\alias{prettyplot}
\alias{refvector}
\alias{get.oneseg.bdry}
\alias{segment1}
 \alias{tumors}
 
\title{Internal Clonality functions}
\description{
  Internal functions of package Clonality.
}
\usage{
LRpv(tum, pp,nref)
LRts (tum,p, MX)
tumors(p,cc,m)
refvector(p,cc,m,nref=1000)
CM.pvalue(rw)
calc.freq(pfreq,refdata, classall,nmad,segmethod,segpar) 
calculateLR(data.seg1,classall,ptlist,pfreq,reference,allpairs=TRUE,gainthres,lossthres,segmethod,segpar)
segment1(xcna,segmethod,segpar)
oneseg(x, alpha, nperm, sbdry) 
get.oneseg.bdry(alpha,nperm)
GL(seg,nmad)
func(ss1,ss2)
complexts(s1,s2,maplocs)
indiv.test(ss1,ss2,func,gainthres,lossthres,Nsim=100,segmethod,segpar)
grantLR(tum1,tum2,p,pi,pc,cvalue=0.5,rescale=TRUE,prnfile=NULL,nm=NULL,chrlist)
class.all(seg1)
prettyplot(datseg,path,nm,lab.general="",t1lab="Tumor 1",t2lab="Tumor 2",
many=TRUE,gains=NULL,losses=NULL)




}
\details{These are not to be called directly by the user}
\keyword{internal}