EVOLUTION-MANAGER
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: LOD support interval</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for lodint {qtl}"><tr><td>lodint {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>LOD support interval</h2> <h3>Description</h3> <p>Calculate a LOD support interval for a particular chromosome, using output from scanone. </p> <h3>Usage</h3> <pre>lodint(results, chr, qtl.index, drop=1.5, lodcolumn=1, expandtomarkers=FALSE)</pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>results</code></td> <td> <p>Output from <code><a href="scanone.html">scanone</a></code>, or a qtl object as output from <code><a href="refineqtl.html">refineqtl</a></code>.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>A chromosome ID (if input <code>results</code> are from <code><a href="scanone.html">scanone</a></code> (should have length 1).</p> </td></tr> <tr valign="top"><td><code>qtl.index</code></td> <td> <p>Numeric index for a QTL (if input <code>results</code> are from <code><a href="refineqtl.html">refineqtl</a></code> (should have length 1).</p> </td></tr> <tr valign="top"><td><code>drop</code></td> <td> <p>LOD units to drop to form the interval.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>An integer indicating which of the LOD score columns should be considered (if input <code>results</code> are from <code><a href="scanone.html">scanone</a></code>).</p> </td></tr> <tr valign="top"><td><code>expandtomarkers</code></td> <td> <p>If TRUE, the interval is expanded to the nearest flanking markers.</p> </td></tr> </table> <h3>Value</h3> <p>An object of class <code>scanone</code> indicating the estimated QTL position and the approximate endpoints for the LOD support interval. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a> </p> <h3>See Also</h3> <p><code><a href="scanone.html">scanone</a></code>, <code><a href="bayesint.html">bayesint</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper, step=0.5) out <- scanone(hyper, method="hk") lodint(out, chr=1) lodint(out, chr=4) lodint(out, chr=4, drop=2) lodint(out, chr=4, expandtomarkers=TRUE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>