process: Optimization wrapper, maximizing either the joint model of...
In rxSeq: Combined Total and Allele Specific Reads Sequencing Study

Description Usage Arguments Value Author(s) See Also Examples

Performs optimization of one of four combinations: joint TReC and ASE or just TReC for autosome or X chromosome and tests with lrt test several hypotheses: additive, parent of origin, dominance, consistency of TreC and ASE additive effect, ASE only additive effect, sex, sex specific additive, dominance deviation for males.

1	process(rc, hessian=FALSE)

`rc`	an object of class readCounts.
`hessian`	a flag whether Hessian matrix for these genes should be calculated, by default set to FALSE

a list of following matrices (if there is only one sex, only the relevant tests and matrices are outputed) :

`pvals`	matrix of p-values from description for each gene corresponding row
`coef.full`	matrix of full model fit coefficients, -log(likelihood at these coefficients),phi, theta (2 overdispersion parameters used)
`coef.add`	matrix of additive restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.poo`	matrix of parent of origin restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.dom`	matrix of dominance restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.same`	matrix of TReC=ASE additive restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.ase.add`	matrix of ASE additive restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.sex`	matrix of sex restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.sex.add`	matrix of sex specific additive restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`coef.dev.dom`	matrix of dominance deviation for male restricted fit coefficients, -log(likelihood at these coefficients),phi, theta
`errorlist`	a list of errors
`hess.lst`	a list of heassian matrices, if parameter hessian is set to TRUE

Vasyl Zhabotynsky vasyl@unc.edu

get.tausB,nLogLik, data.X, data.A, rcA, readCounts.

## Not run: 
# fitting X chromosome data example, for a full model, i.e. assuming we have allele specific reads:
trecase.A.out = process(rc=rcA)
names(trecase.A.out)
trecase.A.out$pval

#alternatively for X chromosome:
trecase.X.out = process(rc=rcX)
names(trecase.X.out)
trecase.X.out$pval

## End(Not run)