startvalue: Start value for maternal allele and haplotype frequencies

In hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

Start value for maternal allele and haplotype frequencies

Description

Determine default start values for Expectation Maximisation (EM) algorithm that is used to estimate paternal recombination rate and maternal haplotype frequencies

Usage

startvalue(Fam1, Fam2, Dd = 0, prec = 1e-06)

Arguments

Fam1	matrix (DIM n.progeny x 2) of progeny genotypes (0, 1, 2) of genomic family with coupling phase sires (1) at SNP pair
Fam2	matrix (DIM n.progeny x 2) of progeny genotypes (0, 1, 2) of genomic family with repulsion phase sires (2) at SNP pair
Dd	maternal LD, default 0
prec	minimum accepted start value for fAA, fAB, fBA; default 1e-6

Value

list (LEN 8)

fAA.start

frequency of maternal haplotype 1-1

fAB.start

frequency of maternal haplotype 1-0

fBA.start

frequency of maternal haplotype 0-1

p1

estimate of maternal allele frequency (allele 1) when sire is heterozygous at SNP1

p2

estimate of maternal allele frequency (allele 1) when sire is heterozygous at SNP2

L1

lower bound of maternal LD

L2

upper bound for maternal LD

critical

0 if parameter estimates are unique; 1 if parameter estimates at both solutions are valid

Examples

 n1 <- 100
 n2 <- 20
 G1 <- matrix(ncol = 2, nrow = n1, sample(c(0:2), replace = TRUE,
  size = 2 * n1))
 G2 <- matrix(ncol = 2, nrow = n2, sample(c(0:2), replace = TRUE,
  size = 2 * n2))
 startvalue(G1, G2)

hsrecombi documentation built on June 7, 2023, 6:02 p.m.