EVOLUTION-MANAGER
Edit File: countXO.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: Count number of obligate crossovers for each individual</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 countXO {qtl}"><tr><td>countXO {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Count number of obligate crossovers for each individual</h2> <h3>Description</h3> <p>Count the number of obligate crossovers for each individual in a cross, either by chromosome or overall. </p> <h3>Usage</h3> <pre> countXO(cross, chr, bychr=FALSE) </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>chr</code></td> <td> <p>Optional vector indicating the chromosomes to investigate. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding <code>-</code> to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.</p> </td></tr> <tr valign="top"><td><code>bychr</code></td> <td> <p>If TRUE, return counts for each individual chromosome; if FALSE, return the overall number across the selected chromosomes.</p> </td></tr> </table> <h3>Details</h3> <p>For each individual we count the minimal number of crossovers that explain the observed genotype data. </p> <h3>Value</h3> <p>If <code>bychr=TRUE</code>, a matrix of counts is returned, with rows corresponding to individuals and columns corresponding to chromosomes. </p> <p>If <code>bychr=FALSE</code>, a vector of counts (the total number of crossovers across all selected chromosomes) is returned. </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="ripple.html">ripple</a></code>, <code><a href="locateXO.html">locateXO</a></code>, <code><a href="cleanGeno.html">cleanGeno</a></code> </p> <h3>Examples</h3> <pre> data(hyper) plot(countXO(hyper)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>