R/ll.jRCI.trec.ase.A2.R

In rxSeq: Combined Total and Allele Specific Reads Sequencing Study

`ll.jRCI.trec.ase.A2` = 
function(par, yi, ind.lst, X, sex=NULL, ni, ni0, xs, iphi, theta)
{
  logL = ll.tRCI.A(par0=c(rep(par[1:2], 2), par[-(1:2)]), yi=yi, ind.lst=ind.lst, X=X, twosex=TRUE, iphi=iphi)
  logL = logL + ll.aRC(par0=c(par[1], par[3]), ni[sex == 1], ni0[sex == 1], xs[sex == 1], theta)
  logL = logL + ll.aRC(par0=c(par[2], par[4]), ni[sex == -1], ni0[sex == -1], xs[sex == -1], theta)

  return(logL)
}