makehap

List of sire haplotypes is set up in the format required for
 hsrecombi. Sire haplotypes are imputed from progeny genotypes using R
 package <code>hsphase</code>.

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. The
implementation relies on paternal half-sib families. If maternal half-sib
families are used, the roles of sire/dam are swapped. Multiple families can
be considered. For parameter estimation, at least one sire has to be double
heterozygous at the investigated pairs of SNPs.
Based on recombination rates, genetic distances between markers can be
estimated. Markers with unusually large recombination rate to markers in
close proximity (i.e. putatively misplaced markers) shall be discarded in
this derivation.
A workflow description is attached as vignette.
*A pipeline is available at GitHub*
<https://github.com/wittenburg/hsrecombi>
Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of
recombination rate and maternal linkage disequilibrium in half-sibs"
<doi:10.3389/fgene.2018.00186>.
Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium
in half-sib families" <doi:10.1534/genetics.111.137521>.

D<c3><b6>rte Wittenburg

hsrecombi

Estimation of Recombination Rate and Maternal LD in Half-Sibs

Dörte Wittenburg

makehap function

<dl><dt>sireID</dt>
<dd>vector (LEN N) of IDs of all sires</dd>
<dt>daughterSire</dt>
<dd>vector (LEN n) of sire ID for each progeny</dd>
<dt>genotype.chr</dt>
<dd>matrix (DIM n x p) of progeny genotypes (0, 1, 2) on a
single chromosome with p SNPs; 9 indicates missing genotype</dd>
<dt>nmin</dt>
<dd>scalar, minimum required number of progeny for proper imputation,
default 30</dd>
<dt>exclude</dt>
<dd>vector (LEN &lt; p) of SNP indices to be excluded from analysis</dd></dl>

Arguments

Make list of imputed sire haplotypes — makehap

<dl>

<dt>sireID</dt>
<dd>vector (LEN N) of IDs of all sires</dd>


<dt>daughterSire</dt>
<dd>vector (LEN n) of sire ID for each progeny</dd>


<dt>genotype.chr</dt>
<dd>matrix (DIM n x p) of progeny genotypes (0, 1, 2) on a
single chromosome with p SNPs; 9 indicates missing genotype</dd>


<dt>nmin</dt>
<dd>scalar, minimum required number of progeny for proper imputation,
default 30</dd>


<dt>exclude</dt>
<dd>vector (LEN &lt; p) of SNP indices to be excluded from analysis</dd>

</dl>

makehap: Make list of imputed sire haplotypes

Description

Usage

Value

Arguments

References

Examples