updog (version 1.1.3)

flexdog_obj_out: Log-likelihood that flexdog maximizes when outliers are present.

Description

Log-likelihood that flexdog maximizes when outliers are present.

Usage

flexdog_obj_out(
  probk_vec,
  out_prop,
  refvec,
  sizevec,
  ploidy,
  seq,
  bias,
  od,
  mean_bias,
  var_bias,
  mean_seq,
  var_seq,
  mean_od,
  var_od
)

Arguments

probk_vec

The kth element is the prior probability of genotype k (when starting to count from 0).

out_prop

The probability of being an outlier.

refvec

A vector of counts of reads of the reference allele.

sizevec

A vector of total counts.

ploidy

The ploidy of the species. Assumed to be the same for each individual.

seq

The starting value of the sequencing error rate.

bias

The starting value of the bias.

od

The starting value of the overdispersion parameter.

mean_bias

The prior mean of the log-bias.

var_bias

The prior variance of the log-bias.

mean_seq

The prior mean of the logit of the sequencing error rate.

var_seq

The prior variance of the logit of the sequencing error rate.

mean_od

The prior mean of the logit of the overdispersion parameter.

var_od

The prior variance of the logit of the overdispersion parameter.

Value

A double. The flexdog objective when outliers = TRUE.

See Also

flexdog_obj for the objective function without outliers.