Simulate Allele Counts for Single Individual - Beta-Binomial Distribution with Overdispersion and Error

This function is used to simulate the frequency of biallelic heterozygous sites assuming a beta-binomial distribution. Here we sample sequence depth from a truncated poisson distribution between a set minimum, maximum, and lambda. Only heterozygous sites are returned. Based on input variables, the sites may be filtered based on the total coverage (filter.coverage), allele sequencing coverage (filter.error), or allele frequency (filter.freq).

Usage

sim.ind.BB.tau(
  mvec,
  avec,
  tau = 0.01,
  error = 0.001,
  s.size = 50000,
  lambda = 11,
  max.coverage = 20,
  min.coverage = 2,
  filter.coverage = TRUE,
  max.depth.quantile.prob = 0.9,
  filter.error = TRUE,
  filter.freq = FALSE,
  trunc = c(0, 0),
  sampled = TRUE
)

Arguments

mvec: Vector of mean values of allele frequency.
avec: Vector of alpha values representing the proportion expected of each mean.
tau: Overdispersion parameter. Defaults to 0.01.
error: Sequencing error rate. Defaults to 0.001.
s.size: Number of biallelic sites to generate. Defaults to 50000. Warning, the number of sites generated will not be the number of sites returned due to filtering steps.
lambda: Set lambda for the truncated poisson distrubtion. Defaults to 11.
max.coverage: Maximum sequencing depth per site. Defaults to 20.
min.coverage: Minimum sequencing depth per site. Defaults to 2.
filter.coverage: Default as TRUE. Filters to only retain sites where total sequencing depth is greater than the provided minimum coverage and less than the max quantile depth (set with the max.depth.quantile.prob).
max.depth.quantile.prob: Maximum depth quantile probability. Defaults to 0.9.
filter.error: Default as TRUE. Filter to only retain sites where allele coverage is greater than the sequencing error rate times the total coverage, but less than one minus the sequencing error rate times the total coverage.
filter.freq: Default as FALSE. When set to true, sites are filtered based on provided trunc.
trunc: List of two values representing the lower and upper bounds, \(c_{L}\) and \(c_{U}\). Defaults as c(0,0) to represent no truncation.
sampled: Default as TRUE. Will randomly sample allele A or allele B, then return a data frame with total coverage and coverage of a randomly sampled allele will be returned.

Value

If sampled = FALSE, a data frame with total coverage, coverage of allele A, and coverage of allele B will be returned. If sampled = TRUE, a data frame with total coverage and coverage of a randomly sampled allele will be returned.