flexdog maximizes.Log-likelihood that flexdog maximizes.
flexdog_obj(
probk_vec,
refvec,
sizevec,
ploidy,
seq,
bias,
od,
mean_bias,
var_bias,
mean_seq,
var_seq,
mean_od,
var_od
)The kth element is the prior probability of genotype k (when starting to count from 0).
A vector of counts of reads of the reference allele.
A vector of total counts.
The ploidy of the species. Assumed to be the same for each individual.
The starting value of the sequencing error rate.
The starting value of the bias.
The starting value of the overdispersion parameter.
The prior mean of the log-bias.
The prior variance of the log-bias.
The prior mean of the logit of the sequencing error rate.
The prior variance of the logit of the sequencing error rate.
The prior mean of the logit of the overdispersion parameter.
The prior variance of the logit of the overdispersion parameter.
The objective (marginal log-likelihood) used in
flexdog_full.