process: 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) :