EVOLUTION-MANAGER
Edit File: mqmfind.marker.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: Fetch significant markers after permutation analysis</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 mqmfind.marker {qtl}"><tr><td>mqmfind.marker {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2> Fetch significant markers after permutation analysis </h2> <h3>Description</h3> <p>Fetch significant makers after permutation analysis. These markers can be used as cofactors for model selection in a forward stepwise approach. </p> <h3>Usage</h3> <pre> mqmfind.marker(cross, mqmscan = NULL, perm = NULL, alpha = 0.05, 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>mqmscan</code></td> <td> <p> Results from either <code><a href="scanone.html">scanone</a></code> or <code><a href="mqmscan.html">mqmscan</a></code> </p> </td></tr> <tr valign="top"><td><code>perm</code></td> <td> <p> a <code>scanoneperm</code> object </p> </td></tr> <tr valign="top"><td><code>alpha</code></td> <td> <p> Threshold value, everything with significance < alpha is reported </p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>Display more output on verbose=TRUE </p> </td></tr> </table> <h3>Value</h3> <p>returns a matrix with at each row a significant marker (determined from the <code>scanoneperm</code> object) and with columns: markername, chr and pos (cM) </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><code><a href="mqmprocesspermutation.html">mqmprocesspermutation</a></code> - Function called to convert results from an mqmpermutation into an scanoneperm object </p> </li> <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> # Use the multitrait dataset data(multitrait) # Set cofactors at each 3th marker cof <- mqmsetcofactors(multitrait,3) # impute missing genotypes multitrait <- fill.geno(multitrait) # log transform the 7th phenotype multitrait <- transformPheno(multitrait, 7) # Bootstrap 50 runs in batches of 10 ## Not run: result <- mqmpermutation(multitrait,scanfunction=mqmscan,cofactors=cof, pheno.col=7,n.perm=50,batchsize=10) ## End(Not run) # Create a permutation object f2perm <- mqmprocesspermutation(result) # What LOD score is considered significant ? summary(f2perm) # Find markers with a significant QTL effect (First run is original phenotype data) marker <- mqmfind.marker(multitrait,result[[1]],f2perm) # Print it to the screen marker </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>