EVOLUTION-MANAGER
Edit File: mqmsetcofactors.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: Set cofactors at fixed intervals, to be used with MQM</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 mqmsetcofactors {qtl}"><tr><td>mqmsetcofactors {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Set cofactors at fixed intervals, to be used with MQM</h2> <h3>Description</h3> <p>Set cofactors, at fixed marker intervals. Together with <code>mqmscan</code> cofactors are selected through backward elimination. </p> <h3>Usage</h3> <pre> mqmsetcofactors(cross, each = NULL, cofactors=NULL, sexfactors=NULL, verbose=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>each</code></td> <td> <p> Every 'each' marker will be used as a cofactor, when each is used the <code>cofactors</code> and <code>sexfactors</code> parameter is ignored </p> </td></tr> <tr valign="top"><td><code>cofactors</code></td> <td> <p>List of cofactors to be analysed in the QTL model. To set cofactors use <code><a href="mqmautocofactors.html">mqmautocofactors</a></code> or <code>mqmsetcofactors</code>; when <code>each</code> is set, this parameter is ignored </p> </td></tr> <tr valign="top"><td><code>sexfactors</code></td> <td> <p> list of markers which should be treated as dominant cofactors (sexfactors), when <code>each</code> is set, this parameter is ignored </p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print tracing information.</p> </td></tr> </table> <h3>Value</h3> <p>An list of cofactors to be passed into <code><a href="mqmscan.html">mqmscan</a></code>. </p> <h3>Author(s)</h3> <p>Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman <a href="mailto:broman@wisc.edu">broman@wisc.edu</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(hyper) # Hyper dataset hyperfilled <- fill.geno(hyper) # Automatic cofactors every third marker cofactors <- mqmsetcofactors(hyperfilled,3) result <- mqmscan(hyperfilled,cofactors) # Backward model selection mqmgetmodel(result) #Manual cofactors at markers 3,6,9,12,40 and 60 cofactors <- mqmsetcofactors(hyperfilled,cofactors=c(3,6,9,12,40,60)) result <- mqmscan(hyperfilled,cofactors) # Backward model selection mqmgetmodel(result) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>