BBB_NMP_pl_subset

A dataset containing real genotype likelihoods in phred scores for 1,000
SNPs. The data is available for ten individuals and the first 1,000 SNPs on
chromosome 1. The data corresponds to a low-fold sequencing experiment. There
are three columns per individuals (for genotypes 00, 01 and 11).

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

BBB_NMP_pl_subset function

A data frame with 1,000 rows and 35 variables:<dl>
 <dt>chr</dt>
<dd>The chromosome number</dd> <dt>marker_name</dt>
<dd>The marker id</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_pl1</dt>
<dd>The AA phred likelihood for the first individual</dd> <dt>id1_pl2</dt>
<dd>The AB phred likelihood for the first individual</dd> <dt>id1_pl3</dt>
<dd>The BB phred likelihood for the first individual</dd> <dt>id2_pl1</dt>
<dd>The AA phred likelihood for the second individual</dd> <dt>id2_pl2</dt>
<dd>The AB phred likelihood for the second individual</dd> <dt>id2_pl3</dt>
<dd>The BB phred likelihood for the second individual</dd> <dt>id3_pl1, id3_pl2, id3_pl3, id4_pl1, id4_pl2, id4_pl3, id5_pl1, id5_pl2, id5_pl3, id6_pl1, id6_pl2, id6_pl3, id7_pl1, id7_pl2, id7_pl3, id8_pl1, id8_pl2, id8_pl3, id9_pl1, id9_pl2, id9_pl3, id10_pl1, id10_pl2, id10_pl3</dt>
<dd>The phred likelihoods for the other individuals</dd>
 
</dl>

Format

Example for "pl" format specification — BBB_NMP_pl_subset

A data frame with 1,000 rows and 35 variables:<dl>
 <dt>chr</dt>
<dd>The chromosome number</dd>

 <dt>marker_name</dt>
<dd>The marker id</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_pl1</dt>
<dd>The AA phred likelihood for the first individual</dd>

 <dt>id1_pl2</dt>
<dd>The AB phred likelihood for the first individual</dd>

 <dt>id1_pl3</dt>
<dd>The BB phred likelihood for the first individual</dd>

 <dt>id2_pl1</dt>
<dd>The AA phred likelihood for the second individual</dd>

 <dt>id2_pl2</dt>
<dd>The AB phred likelihood for the second individual</dd>

 <dt>id2_pl3</dt>
<dd>The BB phred likelihood for the second individual</dd>

 <dt>id3_pl1, id3_pl2, id3_pl3, id4_pl1, id4_pl2, id4_pl3, id5_pl1, id5_pl2, id5_pl3, id6_pl1, id6_pl2, id6_pl3, id7_pl1, id7_pl2, id7_pl3, id8_pl1, id8_pl2, id8_pl3, id9_pl1, id9_pl2, id9_pl3, id10_pl1, id10_pl2, id10_pl3</dt>
<dd>The phred likelihoods for the other individuals</dd>
 
</dl>

BBB_NMP_pl_subset: Example for "pl" format specification

Description

Usage

Arguments

Format