maxLogLikelihoodCalculator1s: Function that given observed count data along a known...

In MBASED: Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

Description

Function that given observed count data along a known haplotype returns a maximum likelihood estimate of the underlying haplotype frequency.

Usage

maxLogLikelihoodCalculator1s(lociHapACounts, lociTotalCounts,
  lociHapANoASEProbs, lociRhos, checkArgs = FALSE)

Arguments

lociHapACounts	counts of haplotype A-supporting reads at individual loci. Must be a vector of non-negative integers.
lociTotalCounts	total read counts of at individual loci. Must be a vector of positive integers.
lociHapANoASEProbs	probabilities of observing haplotype A-supporting reads at individual loci under conditions of no ASE (e.g., vector with all entries set to 0.5, if there is no pre-existing allelic bias at any locus). Must be a vector with entries >0 and <1.
lociRhos	dispersion parameters of beta distribution at individual loci (set to 0 if the read count-generating distribution at the locus is binomial). Must be a numeric vector with entries >=0 and <1.
checkArgs	single boolean specifying whether arguments should be checked for adherence to specifications. DEFAULT: FALSE

Details

Given observed read counts supporting hapltoype A at a collection of loci, the total read counts at those loci, the probablities of observing haplotype A-supporting reads under conditions of no ASE and the dispersion parameters, this function returns a maximum likelihood estimate of the true underlying frequency of haplotype A as well as corresponding value of log-likelihood.

Value

a list with two elements: maximum (MLE of haplotype A frequency) and objective (loglikelihood at MLE). These are the two elements that are output by the optimize() function, which is used internally by the maxLogLikelihoodCalculator1s.

Examples

MBASED:::maxLogLikelihoodCalculator1s(lociHapACounts=c(5, 12), lociTotalCounts=c(10, 24), lociHapANoASEProbs=c(0.5, 0.5), lociRhos=c(0,0))

MBASED documentation built on Nov. 8, 2020, 5:53 p.m.