process {rxSeq} | R Documentation |
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 vasyl@unc.edu
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)