BLUE

Calculation of BLUEs from data frame of genotype names and phenotypes (assuming repeated measurements)

Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.

Peter Bourke

polyqtlR

QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Christine Hackett

Chris Maliepaard

Geert van Geest

Roeland Voorrips

Johan Willemsen

BLUE function

<dl><dt>data</dt>
<dd>Data frame of genotype codes and corresponding phenotypes</dd>
<dt>model</dt>
<dd>The model specification of fixed terms, eg. Yield ~ Clones</dd>
<dt>random</dt>
<dd>The random component of the model (repeat structure, can be nested), eg. ~1 | Blocks if only Blocks are used</dd>
<dt>genotype.ID</dt>
<dd>The colname used to describe genotypes, e.g. "Clones"</dd></dl>

Arguments

Calculate Best Linear Unbiased Estimates using linear mixed model from nlme package — BLUE

<dl>

<dt>data</dt>
<dd>Data frame of genotype codes and corresponding phenotypes</dd>


<dt>model</dt>
<dd>The model specification of fixed terms, eg. Yield ~ Clones</dd>


<dt>random</dt>
<dd>The random component of the model (repeat structure, can be nested), eg. ~1 | Blocks if only Blocks are used</dd>


<dt>genotype.ID</dt>
<dd>The colname used to describe genotypes, e.g. "Clones"</dd>

</dl>

BLUE: Calculate Best Linear Unbiased Estimates using linear mixed model from `nlme` package

Description

Usage

Value

Arguments

Examples