Objective function for updating sequencing error rate, bias, and overdispersion parameters.
obj_for_eps(
parvec,
refvec,
sizevec,
ploidy,
mean_bias,
var_bias,
mean_seq,
var_seq,
mean_od,
var_od,
wmat,
update_bias = TRUE,
update_seq = TRUE,
update_od = TRUE
)A vector of length three. The first element is the sequencing error rate, the second element is the allele bias, and the third element is the overdispersion parameter.
A vector. The ith element is the reference count for the ith individual in the SNP.
A vector. the ith element is the size count for the ith individual in the SNP/
The ploidy of the species.
The prior mean of the log-bias.
The prior variance of the log-bias
The prior mean of the logit sequencing error rate.
The prior variance of the logit sequencing error rate.
The prior mean of the logit of the overdispersion parameter
The prior variance of the logit of the overdispersion parameter.
The matrix of (variational) posterior probabilities for each dosage. The rows index the individuals and the columns index the dosage levels.
A logical. This is not used in obj_for_eps,
but sets the second element to 0.0 in grad_for_eps.
A logical. This is not used in obj_for_eps,
but sets the first element to 0.0 in grad_for_eps.
A logical. This is not used in obj_for_eps,
but sets the third element to 0.0 in grad_for_eps.
A double. The objective when updating eps in
mupdog.