EVOLUTION-MANAGER
Edit File: mqmprocesspermutation.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: Convert mqmmulti objects into a scanoneperm object</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 mqmprocesspermutation {qtl}"><tr><td>mqmprocesspermutation {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Convert mqmmulti objects into a scanoneperm object</h2> <h3>Description</h3> <p>Function to convert <code>mqmmulti</code> objects into a <code>scanoneperm</code> object, this allows the use of R/qtl methods for permutation analysis that do not support the output of a multiple QTL scan using mqm's outputstructure. </p> <h3>Usage</h3> <pre> mqmprocesspermutation(mqmpermutationresult = NULL) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>mqmpermutationresult</code></td> <td> <p><code>mqmmulti</code> object obtained after performing permutations on a single trait.using the function <code><a href="mqmpermutation.html">mqmpermutation</a></code> </p> </td></tr> </table> <h3>Value</h3> <p>Output of the algorithm is a <code>scanoneperm</code> object. See also: <code><a href="summary.scanoneperm.html">summary.scanoneperm</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> # QTL at chromosome 3 f2qtl <- c(3,15,1,0) # Mouse genetic map data(map10) # Simulate a F2 Cross f2cross <- sim.cross(map10,f2qtl,n=100,type="f2") ## Not run: # Bootstrap MQM mapping on the f2cross f2result <- mqmpermutation(f2cross,scanfunction=mqmscan) ## End(Not run) # Create a permutation object f2perm <- mqmprocesspermutation(f2result) # What LOD score is considered significant? summary(f2perm) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>