Estimate Jacquard condensed identity coefficients by identity-by-state (IBS) from genotypic data.

This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.

Riyan Cheng

QTLRel

Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees

ibs function

<dl> <dt>x</dt>
<dd>Genotype data with genotypes ("AA", "AB", "BB", or, 1, 2, 3) and without missing data, or probabilities for these genotypes (e.g., obtained by using <code>genoProb</code>). In case of genotype data, rows represent individuals and columns represent SNPs.</dd></dl>

Arguments

Estimate Jacquard condensed identity coefficients — ibs

<dl>

 <dt>x</dt>
<dd>Genotype data with genotypes ("AA", "AB", "BB", or, 1, 2, 3) and without missing data, or probabilities for these genotypes (e.g., obtained by using <code>genoProb</code>). In case of genotype data, rows represent individuals and columns represent SNPs.</dd>

</dl>

ibs: Estimate Jacquard condensed identity coefficients

Description

Usage

Value

Arguments

See Also