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<html><head><title>R: Quantitative Trait Locus genetic analysis in Heterogeneous
Stocks</title>
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<h1> Quantitative Trait Locus genetic analysis in Heterogeneous
Stocks
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</div><h2>Documentation for package ‘happy’ version 2.1</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
</ul>
<h2>Help Pages</h2>
<table width="100%">
<tr><td width="25%"><a href="mergeprepare.html">condmergefit</a></td>
<td>Perform tests to determine whether individual polymorphisms could have given rise to a QTL</td></tr>
<tr><td width="25%"><a href="epistasis.html">epistasis</a></td>
<td>Analysis of Epistasis between Markers</td></tr>
<tr><td width="25%"><a href="epistasis.html">epistasispair</a></td>
<td>Analysis of Epistasis between Markers</td></tr>
<tr><td width="25%"><a href="mergeprepare.html">fastmergefit</a></td>
<td>Perform tests to determine whether individual polymorphisms could have given rise to a QTL</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.fn</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.gr</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.init</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.iterate</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.loop</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gaussian.null</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="gauss.html">gfit</a></td>
<td>Fit a Gaussian Mixture Model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="AAA-happy.html">happy</a></td>
<td>Quantitative Trait Locus analysis in Heterogeneous Stocks</td></tr>
<tr><td width="25%"><a href="AAA-happy.html">happy.matrices</a></td>
<td>Quantitative Trait Locus analysis in Heterogeneous Stocks</td></tr>
<tr><td width="25%"><a href="AAA-happy.html">happy.save</a></td>
<td>Quantitative Trait Locus analysis in Heterogeneous Stocks</td></tr>
<tr><td width="25%"><a href="happyplot.html">happyplot</a></td>
<td>Plotting functions for happy model fits</td></tr>
<tr><td width="25%"><a href="hdesign.html">hdesign</a></td>
<td>Extract design matrix or genotypes for a specific marker interval from a happy object</td></tr>
<tr><td width="25%"><a href="hfit.html">hfit</a></td>
<td>Fit a model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="hfit.html">hfit.sequential</a></td>
<td>Fit a model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="hdesign.html">hgenotype</a></td>
<td>Extract design matrix or genotypes for a specific marker interval from a happy object</td></tr>
<tr><td width="25%"><a href="hdesign.html">hprob</a></td>
<td>Extract design matrix or genotypes for a specific marker interval from a happy object</td></tr>
<tr><td width="25%"><a href="AAA-happy.html">introduction</a></td>
<td>Quantitative Trait Locus analysis in Heterogeneous Stocks</td></tr>
<tr><td width="25%"><a href="hcache.html">load.genome</a></td>
<td>Save HAPPY design matrices and genotypes to disk for rapid reloading</td></tr>
<tr><td width="25%"><a href="hcache.html">load.markers</a></td>
<td>Save HAPPY design matrices and genotypes to disk for rapid reloading</td></tr>
<tr><td width="25%"><a href="mergematrices.html">mergedpositionmatrix</a></td>
<td>Construct matrices used to merge together founder strains</td></tr>
<tr><td width="25%"><a href="mergeprepare.html">mergefit</a></td>
<td>Perform tests to determine whether individual polymorphisms could have given rise to a QTL</td></tr>
<tr><td width="25%"><a href="mergelist.html">mergelist</a></td>
<td>Create an object descrbing how to merge strains together</td></tr>
<tr><td width="25%"><a href="mergematrices.html">mergematrices</a></td>
<td>Construct matrices used to merge together founder strains</td></tr>
<tr><td width="25%"><a href="happyplot.html">mergeplot</a></td>
<td>Plotting functions for happy model fits</td></tr>
<tr><td width="25%"><a href="mergeprepare.html">mergeprepare</a></td>
<td>Perform tests to determine whether individual polymorphisms could have given rise to a QTL</td></tr>
<tr><td width="25%"><a href="hfit.html">normalise</a></td>
<td>Fit a model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="hfit.html">pfit</a></td>
<td>Fit a model to an object returned by happy()</td></tr>
<tr><td width="25%"><a href="hcache.html">save.genome</a></td>
<td>Save HAPPY design matrices and genotypes to disk for rapid reloading</td></tr>
<tr><td width="25%"><a href="hcache.html">save.happy</a></td>
<td>Save HAPPY design matrices and genotypes to disk for rapid reloading</td></tr>
<tr><td width="25%"><a href="hcache.html">the.chromosomes</a></td>
<td>Save HAPPY design matrices and genotypes to disk for rapid reloading</td></tr>
</table>
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