readGenotype

Reads a genotype file and optionally checks it for common formatting/data issues.

Genotype

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

readGenotype function

<dl> <dt>genotypePath</dt>
<dd><code>character</code>. Path to the genotype file (animals in rows and SNPs in columns).
 SNPs should be coded as <code>0, 1, 2</code> for <code>AA, AB, BB</code>. Use <code>9</code> for missing data.
 Please refer to the vignette for more information.</dd> <dt>separatorGenotype</dt>
<dd><code>character</code>. Field separator used in the genotype file.</dd> <dt>check</dt>
<dd><code>logical</code>. If <code>TRUE</code>, check the genotype file for possible errors.</dd></dl>

Arguments

Read and Check the Genotype File — readGenotype

<dl>

 <dt>genotypePath</dt>
<dd><code>character</code>. Path to the genotype file (animals in rows and SNPs in columns).
 SNPs should be coded as <code>0, 1, 2</code> for <code>AA, AB, BB</code>. Use <code>9</code> for missing data.
 Please refer to the vignette for more information.</dd>

 <dt>separatorGenotype</dt>
<dd><code>character</code>. Field separator used in the genotype file.</dd>

 <dt>check</dt>
<dd><code>logical</code>. If <code>TRUE</code>, check the genotype file for possible errors.</dd>

</dl>

readGenotype: Read and Check the Genotype File

Description

Usage

Value

Arguments