Beta-binomial mixture model log-likelihood derivatives to its parameters involved in optimization

BetaBinomMix_LLDeriv Lorem ipsum

BetaBinomMix_LLDeriv_transfo(
  ref_counts,
  var_counts,
  probshift,
  SE,
  prr,
  pvv,
  prv,
  theta_hom,
  theta_het,
  Der1,
  Der2 = NULL
)

Arguments

ref_counts

Number or Numeric vector Reference count(s).

var_counts

Number or Numeric vector. Variant count(s).

probshift

Number. The reference allele fraction in heterozygotes, indicating allelic bias when deviating from 0.5

SE

Number. Sequencing error rate.

prr

Number. Reference homozygote genotype probability of the locus.

pvv

Number. Variant homozygote genotype probability of the locus.

prv

Number. Heterozygote genotype probability of the locus.

theta_hom

Number. The dispersion parameter of the homozygous peaks.

Der1

String. Derivate with respect to this parameter.

Der2

String. Derivate with respect to this parameter as well; optional.

isCase

Number or Numeric vector. Equals 1 for cases and 0 for controls.

Value

A log-likelihood derivative