Phases the half-sib family by using the blocking structure and imputed sire matrices.

inference

haplotype

reconstruction

phase

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

Mohammad Ferdosi

hsphase

Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data

Cedric Gondro

phf function

<dl> <dt>GenotypeMatrix</dt>
<dd><code>matrix</code> half-sib genotypes (one half-sib per row, with SNP ordered by mapping position in the columns. Data should be numeric. Use 0, 1 and 2 respectively for AA, AB and BB. Use 9 for missing data)</dd> <dt>blockMatrix</dt>
<dd><code>matrix</code> blocking structure (output of <code>bmh</code>)</dd> <dt>sirePhasedMatrix</dt>
<dd><code>matrix</code> imputed sire (output of <code>ssp</code>)</dd></dl>

Arguments

Half-Sib Family Phasing — phf

<dl>

 <dt>GenotypeMatrix</dt>
<dd><code>matrix</code> half-sib genotypes (one half-sib per row, with SNP ordered by mapping position in the columns. Data should be numeric. Use 0, 1 and 2 respectively for AA, AB and BB. Use 9 for missing data)</dd>

 <dt>blockMatrix</dt>
<dd><code>matrix</code> blocking structure (output of <code>bmh</code>)</dd>

 <dt>sirePhasedMatrix</dt>
<dd><code>matrix</code> imputed sire (output of <code>ssp</code>)</dd>

</dl>

phf: Half-Sib Family Phasing

Description

Usage

Value

Arguments

See Also

Examples