EVOLUTION-MANAGER
Edit File: add.threshold.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: Add significance threshold to plot</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 add.threshold {qtl}"><tr><td>add.threshold {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Add significance threshold to plot</h2> <h3>Description</h3> <p>Add a significance threshold to a plot created by <code><a href="plot.scanone.html">plot.scanone</a></code>), using the permutation results. </p> <h3>Usage</h3> <pre> add.threshold(out, chr, perms, alpha=0.05, lodcolumn=1, gap=25, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>out</code></td> <td> <p>An object of class <code>"scanone"</code>, as output by <code><a href="scanone.html">scanone</a></code>. This must be identical to what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector specifying which chromosomes to plot. If a selected subset of chromosomes were plotted, they must be specified here.</p> </td></tr> <tr valign="top"><td><code>perms</code></td> <td> <p>Permutation results from <code><a href="scanone.html">scanone</a></code>, used to calculate the significance threshold.</p> </td></tr> <tr valign="top"><td><code>alpha</code></td> <td> <p>Significance level of the threshold.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>An integer indicating which of column in the permutation results should be used.</p> </td></tr> <tr valign="top"><td><code>gap</code></td> <td> <p>Gap separating chromosomes (in cM). This must be identical to what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to the function <code><a href="../../graphics/html/abline.html">abline</a></code> when it is called.</p> </td></tr> </table> <h3>Details</h3> <p>This function allows you to add a horizontal line at the significance threshold to genome scan results plotted by <code><a href="plot.scanone.html">plot.scanone</a></code>. </p> <p>The arguments <code>out</code>, <code>chr</code>, and <code>gap</code> must match what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>. </p> <p>The argument <code>perms</code> must be specified. If X-chromosome-specific permutations were performed (via the argument <code>perm.Xsp</code> in the call to <code><a href="scanone.html">scanone</a></code>), separate thresholds will be plotted for the autosomes and the X chromosome. These are calculated via the <code><a href="summary.scanoneperm.html">summary.scanoneperm</a></code> function. </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="scanone.html">scanone</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code>, <code><a href="summary.scanoneperm.html">summary.scanoneperm</a></code>, <code><a href="xaxisloc.scanone.html">xaxisloc.scanone</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper) out <- scanone(hyper, method="hk") operm <- scanone(hyper, method="hk", n.perm=100, perm.Xsp=TRUE) plot(out, chr=c(1,4,6,15,"X")) add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.05) add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.1, col="green", lty=2) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>