hsrecombi {hsrecombi}

Estimation of recombination rate and maternal LD

Description

Wrapper function for estimating recombination rate and maternal linkage disequilibrium between intra-chromosomal SNP pairs by calling EM algorithm

Usage

hsrecombi(hap, genotype.chr, exclude = NULL, only.adj = FALSE, prec = 1e-06)

Arguments

hap

list (LEN 2) of lists

famID

list (LEN number of sires) of vectors (LEN n.progeny) of progeny indices relating to lines in genotype matrix

sireHap

list (LEN number of sires) of matrices (DIM 2 x p) of sire haplotypes (0, 1) on investigated chromosome

genotype.chr

matrix (DIM n x p) of all progeny genotypes (0, 1, 2) on a chromosome with p SNPs; 9 indicates missing genotype

exclude

vector (LEN < p) of SNP IDs (for filtering column names of genotype.chr) to be excluded from analysis (default NULL)

only.adj

logical; if TRUE, recombination rate is calculated only between neighbouring markers

prec

scalar; precision of estimation

Details

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.

Value

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

ID of 1. SNP

SNP2

ID of 2. SNP

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 SNP1

p2

Maternal allele frequency (allele 1) at SNP2

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 post-processing function "editraw"

Afterwards, solutions are compared and processed with function editraw, yielding the final estimates for each valid pair of SNPs.

References

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.

Examples

  ### 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)
  ### post-processing to achieve final and valid set of estimates
  final <- editraw(res, map.chr)