impute

Impute the paternal strand from low density to high density utilising high density sire haplotype.

Low_Density

High_Density

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

impute function

<dl><dt>halfsib_genotype_ld</dt>
<dd><code>matrix</code>
half-sib genotypes with low density marker (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>sire_hd</dt>
<dd><code>matrix</code>
haplotype of sire (this parameter can be sequence data or any phased sire - the matrix should have rownames which are the sample
 IDs and colnames which are the SNP names)</dd>
<dt>bmh_forwardVectorSize</dt>
<dd><code>integer</code> number of heterozygous sites used to validate recombination events or check for genotyping errors</dd><dt>bmh_excludeFP</dt>
<dd><code>logical</code> exclude SNPs that may cause heterozygous sites in the sire due to genotyping errors or map errors</dd><dt>bmh_nsap</dt>
<dd><code>integer</code> number of SNPs per block</dd></dl>

Arguments

Impute of Low Density SNP Marker to High Density (Paternal Strand) — impute

<dl>

<dt>halfsib_genotype_ld</dt>
<dd><code>matrix</code>
half-sib genotypes with low density marker (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>sire_hd</dt>
<dd><code>matrix</code>
haplotype of sire (this parameter can be sequence data or any phased sire - the matrix should have rownames which are the sample
 IDs and colnames which are the SNP names)</dd>


<dt>bmh_forwardVectorSize</dt>
<dd><code>integer</code> number of heterozygous sites used to validate recombination events or check for genotyping errors</dd>



<dt>bmh_excludeFP</dt>
<dd><code>logical</code> exclude SNPs that may cause heterozygous sites in the sire due to genotyping errors or map errors</dd>



<dt>bmh_nsap</dt>
<dd><code>integer</code> number of SNPs per block</dd>

</dl>

impute: Impute of Low Density SNP Marker to High Density (Paternal Strand)

Description

Usage

Value

Arguments

See Also