EVOLUTION-MANAGER
Edit File: plot.scantwoperm.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: Plot permutation results for a 2d, 2-QTL genome scan</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 plot.scantwoperm {qtl}"><tr><td>plot.scantwoperm {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot permutation results for a 2d, 2-QTL genome scan</h2> <h3>Description</h3> <p>Plot a histogram of the permutation results from a two-dimensional, two-QTL genome scan. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scantwoperm' plot(x, lodcolumn=1, include_rug=TRUE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>"scantwoperm"</code>, as output by <code><a href="scantwo.html">scantwo</a></code> when <code>n.perm</code> is specified.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>This indicates the LOD score column to plot. This should be a single number between 1 and the number of LOD columns in the object input.</p> </td></tr> <tr valign="top"><td><code>include_rug</code></td> <td> <p>If TRUE, include a call to <code><a href="../../graphics/html/rug.html">rug</a></code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to the function <code><a href="../../graphics/html/hist.html">hist</a></code> when it is called.</p> </td></tr> </table> <h3>Details</h3> <p>The function plots a histogram of the permutation results obtained by <code><a href="scantwo.html">scantwo</a></code> when <code>n.perm</code> is specified. Separate histograms are provided for the five LOD scores, <code>full</code>, <code>fv1</code>, <code>int</code>, <code>add</code>, and <code>av1</code>. </p> <h3>Value</h3> <p>None.</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="scantwo.html">scantwo</a></code>, <code><a href="summary.scantwoperm.html">summary.scantwoperm</a></code> </p> <h3>Examples</h3> <pre> data(fake.bc) fake.bc <- calc.genoprob(fake.bc) operm2 <- scantwo(fake.bc, method="hk", n.perm=10) plot(operm2) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>