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Edit File: comparegeno.html
<!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: Compare individuals' genotype data</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 comparegeno {qtl}"><tr><td>comparegeno {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Compare individuals' genotype data</h2> <h3>Description</h3> <p>Count proportion of matching genotypes between all pairs of individuals, to look for unusually closely related individuals. </p> <h3>Usage</h3> <pre>comparegeno(cross, what=c("proportion","number","both"))</pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>cross</code></td> <td> <p>An object of class <code>cross</code>. See <code><a href="read.cross.html">read.cross</a></code> for details.</p> </td></tr> <tr valign="top"><td><code>what</code></td> <td> <p>Indicates whether to return the proportion or number of matching genotypes (or both).</p> </td></tr> </table> <h3>Value</h3> <p>A matrix whose (i,j)th element is the proportion or number of matching genotypes for individuals i and j. </p> <p>If called with <code>what="both"</code>, the lower triangle contains the proportion and the upper triangle contains the number. </p> <p>If called with <code>what="proportion"</code>, the diagonal contains missing values. Otherwise, the diagonal contains the number of typed markers for each individual. </p> <p>The output is given class <code>"comparegeno"</code> so that appropriate <code>summary</code> and <code>plot</code> functions may be used. </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="nmissing.html">nmissing</a></code>, <code><a href="summary.comparegeno.html">summary.comparegeno</a></code>, <code><a href="plot.comparegeno.html">plot.comparegeno</a></code> </p> <h3>Examples</h3> <pre> data(listeria) cg <- comparegeno(listeria) summary(cg, 0.7) plot(cg) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>