typs

A dataset containing real genotypes for 6 individuals.
Genotypes are available for a low density array with 6370 SNPs on 29 autosomes.
The six last columns correspond to the genotypes.
Missing genotypes are set to 9.

datasets

Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.

Tom Druet

RZooRoH

Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes

typs function

A data frame with 6370 rows and 10 variables:<dl>
<dt>chr</dt>
<dd>The chromosome number</dd><dt>pos</dt>
<dd>The position of the marker</dd><dt>allele1</dt>
<dd>The name of the first marker allele</dd><dt>allele2</dt>
<dd>The name of the second marker allele</dd><dt>id1</dt>
<dd>The genotypes for the first individuals (id1)</dd><dt>id2</dt>
<dd>The genotypes for the second individuals (id2)</dd><dt>id3</dt>
<dd>The genotypes for the third individuals (id3)</dd><dt>id4</dt>
<dd>The genotypes for the fourth individuals (id4)</dd><dt>id5</dt>
<dd>The genotypes for the fifth individuals (id5)</dd><dt>id6</dt>
<dd>The genotypes for the sixth individuals (id6)</dd>
</dl>

Format

Subset of a dataset with genotypes for 6 individuals from a cattle population. — typs

A data frame with 6370 rows and 10 variables:<dl>
<dt>chr</dt>
<dd>The chromosome number</dd>

<dt>pos</dt>
<dd>The position of the marker</dd>

<dt>allele1</dt>
<dd>The name of the first marker allele</dd>

<dt>allele2</dt>
<dd>The name of the second marker allele</dd>

<dt>id1</dt>
<dd>The genotypes for the first individuals (id1)</dd>

<dt>id2</dt>
<dd>The genotypes for the second individuals (id2)</dd>

<dt>id3</dt>
<dd>The genotypes for the third individuals (id3)</dd>

<dt>id4</dt>
<dd>The genotypes for the fourth individuals (id4)</dd>

<dt>id5</dt>
<dd>The genotypes for the fifth individuals (id5)</dd>

<dt>id6</dt>
<dd>The genotypes for the sixth individuals (id6)</dd>


</dl>

typs: Subset of a dataset with genotypes for 6 individuals from a cattle population.

Description

Usage

Arguments

Format