LDHScpp {hsrecombi}

Expectation Maximisation (EM) algorithm

Description

Expectation Maximisation (EM) algorithm

Usage

LDHScpp(XGF1, XGF2, fAA, fAB, fBA, theta, display, threshold)

Arguments

XGF1

integer matrix of progeny genotypes in genomic family 1

XGF2

integer matrix of progeny genotypes in genomic family 2

fAA

frequency of maternal haplotype 1-1

fAB

frequency of maternal haplotype 1-0

fBA

frequency of maternal haplotype 0-1

theta

paternal recombination rate

display

logical for displaying additional information

threshold

convergence criterion

Value

list of parameter estimates

D

maternal LD

fAA

frequency of maternal haplotype 1-1

fAB

frequency of maternal haplotype 1-0

fBA

frequency of maternal haplotype 0-1

fBB

frequency of maternal haplotype 0-0

p1

Maternal allele frequency (allele 1) at 1. SNP

p2

Maternal allele frequency (allele 1) at 2. SNP

nfam1

size of genomic family 1

nfam2

size of genomic family 2

error

0 if computations were without error; 1 if EM algorithm did not converge

iteration

number of EM iterations

theta

paternal recombination rate

r2

r^2 of maternal LD

logL

value of log likelihood function