MBASED (version 1.6.0)

estimateMAF2s: Function that given observed count data returns a maximum likelihood estimate of the underlying haplotype frequency. Both situations where the haplotype are known and unknown are handled. In the latter case, likelihood is further maximized over all possible assignments of alleles to haplotypes.

Description

Function that given observed count data returns a maximum likelihood estimate of the underlying haplotype frequency. Both situations where the haplotype are known and unknown are handled. In the latter case, likelihood is further maximized over all possible assignments of alleles to haplotypes.

Usage

estimateMAF2s(lociAllele1CountsSample1, lociTotalCountsSample1, lociAllele1CountsSample2, lociTotalCountsSample2, lociAllele1NoASEProbsSample1, lociAllele1NoASEProbsSample2, lociRhosSample1, lociRhosSample2, isPhased = FALSE, checkArgs = FALSE)

Arguments

lociAllele1CountsSample1,lociAllele1CountsSample2

counts of allele1-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.

lociAllele1NoASEProbsSample1,lociAllele1NoASEProbsSample2

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

isPhased

single boolean specifying whether the phasing has already been performed, in which case the lociAllele1CountsSample1 (and, therefore, lociAllele1CountsSample2) represent the same haplotype. If FALSE (DEFAULT), likelihood is further maximized over all possible assignments of alleles to haplotypes.

checkArgs

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

Value

a list with two elements: MAF (MLE of major allele frequency) and allele1IsMajor (whether allele1 is assigned to haplotype corresponding to maximum likleihood MAF).

Details

Given observed read counts supporting allele1 at a collection of loci in two samples, the total read counts at those loci, the probablities of observing allele1-supporting reads under conditions of no ASE and the dispersion parameters, this function returns a maximum likelihood estimate of the major haplotype frequency as well as corresponding assignment of alleles to haplotypes.

Examples

MBASED:::estimateMAF2s(lociAllele1CountsSample1=c(5, 24), lociTotalCountsSample1=c(15, 36), lociAllele1CountsSample2=c(15, 44), lociTotalCountsSample2=c(45, 66), lociAllele1NoASEProbsSample1=c(0.5, 0.5), lociAllele1NoASEProbsSample2=c(0.5, 0.5), lociRhosSample1=c(0,0), lociRhosSample2=c(0,0), isPhased=TRUE)
MBASED:::estimateMAF2s(lociAllele1CountsSample1=c(5, 12), lociTotalCountsSample1=c(15, 36), lociAllele1CountsSample2=c(15, 22), lociTotalCountsSample2=c(45, 66), lociAllele1NoASEProbsSample1=c(0.5, 0.5), lociAllele1NoASEProbsSample2=c(0.5, 0.5), lociRhosSample1=c(0,0), lociRhosSample2=c(0,0), isPhased=FALSE)