covUnstr

covPW

Compute unstructured covariance pairwise using <code>covPairwise</code> or using a
single model using <code>covUnstr</code>.

internal

Fast multi-trait and multi-trail Genome Wide Association Studies
(GWAS) following the method described in Zhou and Stephens. (2014),
<doi:10.1038/nmeth.2848>. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments
developed by Biometris.

Bart-Jan van Rossum

statgenQTLxT

Multi-Trait and Multi-Trial Genome Wide Association Studies

Willem Kruijer

Fred van Eeuwijk

Martin P Boer

Daniela Bustos-Korts

Emilie J Millet

Joao Paulo

Maikel Verouden

Ron Wehrens

Choazhi Zheng

covUnstr function

<dl><dt>Y</dt>
<dd>An n x p matrix of observed phenotypes, on p traits or trials
for n individuals. No missing values are allowed.</dd>
<dt>K</dt>
<dd>An n x n kinship matrix.</dd>
<dt>X</dt>
<dd>An n x c covariate matrix, c being the number of covariates and n
being the number of genotypes.</dd>
<dt>fixDiag</dt>
<dd>Should the diagonal of the covariate matrix be fixed during
calculations? -- NOT YET IMPLEMENTED</dd>
<dt>VeDiag</dt>
<dd>Should Ve be a diagonal matrix?</dd>
<dt>corMat</dt>
<dd>Should the output be a correlation matrix instead of a
covariance matrix?</dd>
<dt>parallel</dt>
<dd>Should the computation of variance components be done in
parallel?</dd></dl>

Arguments

Compute unstructured covariance — covUnstr

<dl>

<dt>Y</dt>
<dd>An n x p matrix of observed phenotypes, on p traits or trials
for n individuals. No missing values are allowed.</dd>


<dt>K</dt>
<dd>An n x n kinship matrix.</dd>


<dt>X</dt>
<dd>An n x c covariate matrix, c being the number of covariates and n
being the number of genotypes.</dd>


<dt>fixDiag</dt>
<dd>Should the diagonal of the covariate matrix be fixed during
calculations? -- NOT YET IMPLEMENTED</dd>


<dt>VeDiag</dt>
<dd>Should Ve be a diagonal matrix?</dd>


<dt>corMat</dt>
<dd>Should the output be a correlation matrix instead of a
covariance matrix?</dd>


<dt>parallel</dt>
<dd>Should the computation of variance components be done in
parallel?</dd>

</dl>

Compute unstructured covariance

covUnstr: Compute unstructured covariance

Description

Usage

Value

Arguments