EVOLUTION-MANAGER
Edit File: add.cim.covar.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: Indicate marker covariates from composite interval mapping</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.cim.covar {qtl}"><tr><td>add.cim.covar {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Indicate marker covariates from composite interval mapping</h2> <h3>Description</h3> <p>Add dots at the locations of the selected marker covariates, for a plot of composite interval mapping results. </p> <h3>Usage</h3> <pre> add.cim.covar(cimresult, chr, gap=25, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>cimresult</code></td> <td> <p>Composite interval mapping results, as output from <code><a href="cim.html">cim</a></code>.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector specifying which chromosomes to plot. (The chromosomes must be specified by name.) This should be identical to that used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>gap</code></td> <td> <p>Gap separating chromosomes (in cM). This should be identical to that 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>Additional plot arguments, passed to the function <code><a href="../../graphics/html/points.html">points</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>One must first have used the function <code><a href="plot.scanone.html">plot.scanone</a></code> to plot the composite interval mapping results. </p> <p>The arguments <code>chr</code> and <code>gap</code> must be identical to the values used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>. </p> <p>Dots indicating the locations of the selected marker covariates are displayed on the x-axis. (By default, solid red circles are plotted; this may be modified by specifying the graphics parameters <code>pch</code> and <code>col</code>.) </p> <h3>Value</h3> <p>A data frame indicating the marker covariates that were plotted. </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="cim.html">cim</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code> </p> <h3>Examples</h3> <pre> ## Not run: data(hyper) hyper <- calc.genoprob(hyper, step=2.5) out <- scanone(hyper) out.cim <- cim(hyper, n.marcovar=3) plot(out, out.cim, chr=c(1,4,6,15), col=c("blue", "red")) add.cim.covar(out.cim, chr=c(1,4,6,15)) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>