Description Usage Arguments Details Value References Examples
Wrapper function for estimating recombination rate and maternal linkage disequilibrium between intrachromosomal SNP pairs by calling EM algorithm
1  hsrecombi(hap, genotype.chr, snp.chr, only.adj = FALSE, prec = 1e06)

hap 
list (LEN 2) of lists

genotype.chr 
matrix (DIM n x p) of all progeny genotypes (0, 1, 2) on a chromosome with p SNPs 
snp.chr 
vector(LEN p) of SNP indices as in physical map 
only.adj 
logical; if 
prec 
scalar; precision of estimation 
Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers (such as single nucleotide polymorphisms; SNPs) from progeny genotypes and sire haplotypes. At least one sire has to be double heterozygous at the investigated pairs of SNPs. All progeny are merged in two genomic families: (1) coupling phase family if sires are double heterozygous 00/11 and (2) repulsion phase family if sires are double heterozygous 01/10. So far it is recommended processing the chromosomes separately. If maternal halfsib families are used, the roles of sire/dam are swapped. Multiple families can be considered.
list (LEN p  1) of data.frames; for each SNP, parameters are estimated with all following SNPs; two solutions (prefix sln1 and sln2) are obtained for two runs of the EM algorithm
SNP1
index 1. SNP
SNP2
index 2. SNP
D
maternal LD
fAA
frequency of maternal haplotype 11
fAB
frequency of maternal haplotype 10
fBA
frequency of maternal haplotype 01
fBB
frequency of maternal haplotype 00
p1
Maternal allele frequency (allele 1)
p2
Maternal allele frequency (allele 0)
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
unimodal
1 if likelihood is unimodal; 0 if likelihood is bimodal
critical
0 if parameter estimates are unique; 1 if parameter estimates at both solutions are valid, then decision process follows in postprocessing function "editraw"
Afterwards, solutions are compared and processed with function
editraw
, yielding the final estimates for each valid pair of SNPs.
Hampel, A., Teuscher, F., GomezRaya, L., Doschoris, M. & Wittenburg, D. (2018) Estimation of recombination rate and maternal linkage disequilibrium in halfsibs. Frontiers in Genetics 9:186. doi: 10.3389/fgene.2018.00186
GomezRaya, L. (2012) Maximum likelihood estimation of linkage disequilibrium in halfsib families. Genetics 191:195213.
1 2 3 4 5 6 7 8  ### test data
data(targetregion)
### make list for paternal halfsib families
hap < makehaplist(daughterSire, hapSire)
### parameter estimates on a chromosome
res < hsrecombi(hap, genotype.chr, map.chr$SNP)
### postprocessing to achieve final and valid set of estimates
final < editraw(res, map.chr)

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