genosim

A dataset containing simulated genotypes for 20 individuals. Genotypes are
available for 10,000 SNPs on 10 chromosomes. The ten last columns correspond
to the genotypes.

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

genosim function

A data frame with 10,000 rows and 24 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 genotype for the first individual</dd> <dt>id2</dt>
<dd>The genotype for the second individual</dd> <dt>id3, id4, id5, id6, id7, id8, id9, id10, id11, id12, id13, id14, id15, id16, id17, id18, id19, id20</dt>
<dd>The genotypes of the remaining individuals</dd> 
</dl>

Format

Example from a small simulated data set — genosim

A data frame with 10,000 rows and 24 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 genotype for the first individual</dd>

 <dt>id2</dt>
<dd>The genotype for the second individual</dd>

 <dt>id3, id4, id5, id6, id7, id8, id9, id10, id11, id12, id13, id14, id15, id16, id17, id18, id19, id20</dt>
<dd>The genotypes of the remaining individuals</dd>

 
</dl>

genosim: Example from a small simulated data set

Description

Usage

Arguments

Format