EVOLUTION-MANAGER
Edit File: mqmplotcistrans.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: cis-trans 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 mqmplot.cistrans {qtl}"><tr><td>mqmplot.cistrans {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>cis-trans plot</h2> <h3>Description</h3> <p>Plot results for a genomescan using a multiple-QTL model. With genetic location for the traits it is possible to show cis- and trans- locations, and detect trans-bands </p> <h3>Usage</h3> <pre> mqmplot.cistrans(result, cross, threshold=5, onlyPEAK=TRUE, highPEAK=FALSE, cisarea=10, pch=22, cex=0.5, verbose=FALSE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>result</code></td> <td> <p>An object of class <code>mqmmulti</code>. See <code><a href="mqmscanall.html">mqmscanall</a></code> for details.</p> </td></tr> <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>threshold</code></td> <td> <p> Threshold value in LOD, Markers that have a LOD score above this threshold are plotted as small squares (see <code>pch</code> parameter). The markers with LODscores below this threshold are not visible </p> </td></tr> <tr valign="top"><td><code>onlyPEAK</code></td> <td> <p> Plot only the peak markers ? (TRUE/FALSE) (Peak markers are markers that have a QTL likelihood above <code>threshold</code> and higher than other markers in the same region) </p> </td></tr> <tr valign="top"><td><code>highPEAK</code></td> <td> <p> Highlight peak markers ? (TRUE/FALSE). When using this option peak markers (the marker with the highest LOD score in a region above the threshold gets an 25% increase in size and is displayed in red) </p> </td></tr> <tr valign="top"><td><code>cisarea</code></td> <td> <p> Adjust the two green lines around the line y=x </p> </td></tr> <tr valign="top"><td><code>pch</code></td> <td> <p> What kind of character is used in plotting of the figure (Default: 22, small square) </p> </td></tr> <tr valign="top"><td><code>cex</code></td> <td> <p> Size of the points plotted (default to 0.5 half of the original size)</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, give verbose output</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p> Extra parameters will be passed to points </p> </td></tr> </table> <h3>Value</h3> <p>Plotting routine, so no return </p> <h3>Author(s)</h3> <p>Danny Arends <a href="mailto:danny.arends@gmail.com">danny.arends@gmail.com</a> </p> <h3>See Also</h3> <ul> <li><p> The MQM tutorial: <a href="https://rqtl.org/tutorials/MQM-tour.pdf">https://rqtl.org/tutorials/MQM-tour.pdf</a> </p> </li> <li> <p><code><a href="MQM.html">MQM</a></code> - MQM description and references </p> </li> <li> <p><code><a href="mqmscan.html">mqmscan</a></code> - Main MQM single trait analysis </p> </li> <li> <p><code><a href="mqmscanall.html">mqmscanall</a></code> - Parallellized traits analysis </p> </li> <li> <p><code><a href="mqmaugment.html">mqmaugment</a></code> - Augmentation routine for estimating missing data </p> </li> <li> <p><code><a href="mqmautocofactors.html">mqmautocofactors</a></code> - Set cofactors using marker density </p> </li> <li> <p><code><a href="mqmsetcofactors.html">mqmsetcofactors</a></code> - Set cofactors at fixed locations </p> </li> <li> <p><code><a href="mqmpermutation.html">mqmpermutation</a></code> - Estimate significance levels </p> </li> <li> <p><code><a href="scanone.html">scanone</a></code> - Single QTL scanning </p> </li></ul> <h3>Examples</h3> <pre> data(multitrait) data(locations) multiloc <- addloctocross(multitrait,locations) multiloc <- calc.genoprob(multiloc) results <- scanall(multiloc, method="hk") mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>