Model Selection - Expectation Maximization - Beta-Binomial Mixture

This function uses the expectation maximization of both the beta-binomial and beta-binomial-uniform mixture models for model selection. Here we can run up to 32 mixture models.

Usage

quackBetaBinom(
  xm,
  samplename,
  cores,
  parallel = FALSE,
  trunc = c(0, 0),
  lowvar = FALSE,
  tau = NA,
  error = NA,
  free = FALSE
)

Arguments

xm

Matrix with two columns with total coverage and coverage for a randomly sampled allele.

samplename

Name of sample to be included in output.

cores

Threads available to run process in parallel.

parallel

default = FALSE, set to true if cores > 1.

trunc

List of two values representing the lower and upper bounds for allele frequency truncation , \(c_{L}\) and \(c_{U}\). If allele frequency truncation was done to remove error, then you do not need to truncate the expected. If no truncation has been done, this should be set to c(0,0), which is the default.

lowvar

Default to FALSE. When false, variance is equal to 0.01. If set to TRUE and tau and error are not provided, the variance will be set as 0.001.

tau

Sequencing overdispersion parameter. If tau and error are provided, the variance of each mixture will be inferred from these values. If not, the variance by default is equal to 0.01 or 0.001.

error

Sequencing error rate. If tau and error are provided, the variance of each mixture will be inferred from these values. If not, the variance by default is equal to 0.01 or 0.001.

free

default = FALSE, skip the free model calculation and does not calculate delta log-likelihood.

Value

BIC scores and log-likelihood (LL) mixture models including diploid, triploid, tetraploid, pentaploid, and hexaploid. When free = TRUE, the delta log-likelihood (dLL) is calculated based on the associated free model (without or with a uniform mixture). For BIC or delta-log likelihood, the smallest score is the most likely model. For LL, the largest score is the most likely model.