Creates an objective function for peak height data
create.likelihood.vectors.peaks(hypothesis, addAttr=FALSE,
likeMatrix=FALSE, diagnose=FALSE,…)Hypothesis for which to create the objective function
Whether to add attributes to the objective functions. There are two attributes: (1) “hypothesis” referencing the input hypothesis, (ii) ‘functions’ containing the individual objective functions per Locus. The latter contain further attributes.
Whether to return likelihoods for every genotype combination, or
a likelihood summed over all genotypes after optimisation. Set to TRUE
for individual genotype likelihoods. This is used for
get.likely.genotypes.peaks.
Logical. If TRUE returns a list of peak heights,
estimated mean peak height and peak height standard deviation
for each genotype combination. This can be used to obtain Z values
for each fitted peak.
Any named parameter to modify the hypothesis, e.g.
nUnknowns
A function
The objective function is created from the hypothesis. Itself, it takes as arguments the nuisance parameters and, optionally, the parameters for the penalty function. This particular flavor of the objective returns a list containing two items: (i) the likelihoods per locus, (ii) the penalties per locus.
get.likely.genotypes.peaks, penalties.peaks, Objective Functions