Clonality-internal {Clonality} | R Documentation

## 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

[Package Clonality version 1.40.0 Index]