startvalue {hsrecombi} | R Documentation |
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
|
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)