MBASED (version 1.6.0)

logLikelihoodCalculator2s: Function that given observed count data along a known haplotype returns a function that can calculate the likelihood of observing that data for a supplied underlying haplotype frequency.

Description

Function that given observed count data along a known haplotype returns a function that can calculate the likelihood of observing that data for a supplied underlying haplotype frequency.

Usage

logLikelihoodCalculator2s(lociHapACountsSample1, lociTotalCountsSample1, lociHapACountsSample2, lociTotalCountsSample2, lociHapANoASEProbsSample1, lociHapANoASEProbsSample2, lociRhosSample1, lociRhosSample2, checkArgs = FALSE)

Arguments

lociHapACountsSample1,lociHapACountsSample2

counts of haplotype A-supporting reads at individual loci in sample1 and sample2, respectively. Both arguments must be vectors of non-negative integers.

lociTotalCountsSample1,lociTotalCountsSample2

total read counts of at individual loci in sample1 and sample2, respectively. Both arguments must be vectors of non-negative integers.

lociHapANoASEProbsSample1,lociHapANoASEProbsSample2

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) in sample1 and sample2, respectively. Both arguments must be vectors with entries >0 and

lociRhosSample1,lociRhosSample2

dispersion parameters of beta distribution at individual loci (set to 0 if the read count-generating distribution at the locus is binomial) in sample1 and sample2, respectively. Both arguments must be vectors with entries >=0 and

checkArgs

single boolean specifying whether arguments should be checked for adherence to specifications. DEFAULT: FALSE

Value

a function of a single argument pHapA that calculates log likelihood of the observed data if the true underlying haplotype A frequency is pHapA.

Details

Given observed read counts supporting hapltoype A at a collection of loci in two samples, 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 function of a single argument, pHapA, that calculates the likelihood of observing the given haplotype A-supporting counts under the assumption that the true underlying frequency of haplotype A is pHapA.

Examples

LLC <- MBASED:::logLikelihoodCalculator2s(lociHapACountsSample1=c(5, 12), lociTotalCountsSample1=c(15, 36), lociHapACountsSample2=c(15, 22), lociTotalCountsSample2=c(45, 66), lociHapANoASEProbsSample1=c(0.5, 0.5), lociHapANoASEProbsSample2=c(0.5, 0.5), lociRhosSample1=c(0,0), lociRhosSample2=c(0,0))
LLC(1/3) ## the MLE estimate of hapA frequency
LLC(0.9) ## highly implausible value of pHapA
LLC (0.334)