Wrapper function for estimating recombination rate and maternal linkage disequilibrium between intra-chromosomal SNP pairs by calling EM algorithm
list (LEN 2) of lists
matrix (DIM n x p) of all progeny genotypes (0, 1, 2) on a chromosome with p SNPs
vector(LEN p) of SNP indices as in physical map
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 0-0/1-1 and (2) repulsion phase family if sires are double heterozygous 0-1/1-0. So far it is recommended processing the chromosomes separately. If maternal half-sib 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
index 1. SNP
index 2. SNP
frequency of maternal haplotype 1-1
frequency of maternal haplotype 1-0
frequency of maternal haplotype 0-1
frequency of maternal haplotype 0-0
Maternal allele frequency (allele 1)
Maternal allele frequency (allele 0)
size of genomic family 1
size of genomic family 2
0 if computations were without error; 1 if EM algorithm did not converge
number of EM iterations
paternal recombination rate
r^2 of maternal LD
value of log likelihood function
1 if likelihood is unimodal; 0 if likelihood is bimodal
0 if parameter estimates are unique; 1 if parameter estimates at both solutions are valid, then decision process follows in post-processing 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., Gomez-Raya, L., Doschoris, M. & Wittenburg, D. (2018) Estimation of recombination rate and maternal linkage disequilibrium in half-sibs. Frontiers in Genetics 9:186. doi: 10.3389/fgene.2018.00186
Gomez-Raya, L. (2012) Maximum likelihood estimation of linkage disequilibrium in half-sib families. Genetics 191:195-213.
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### test data data(targetregion) ### make list for paternal half-sib families hap <- makehaplist(daughterSire, hapSire) ### parameter estimates on a chromosome res <- hsrecombi(hap, genotype.chr, map.chr$SNP) ### post-processing to achieve final and valid set of estimates final <- editraw(res, map.chr)
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