process {rxSeq}

Optimization wrapper, maximizing either the joint model of total (TReC) and allele specific (ASE) counts or just TReC

Description

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.

Usage

process(rc, hessian=FALSE)

Arguments

rc

an object of class readCounts.

hessian

a flag whether Hessian matrix for these genes should be calculated, by default set to FALSE

Value

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

Author(s)

Vasyl Zhabotynsky [e-mail]

See Also

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

Examples

## 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)