EVOLUTION-MANAGER
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<!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: Parallelized MQM on multiple phenotypes in a cross 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 mqmscanall {qtl}"><tr><td>mqmscanall {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Parallelized MQM on multiple phenotypes in a cross object</h2> <h3>Description</h3> <p>Parallelized QTL analysis using MQM on multiple phenotypes in a cross object (uses SNOW) </p> <h3>Usage</h3> <pre> mqmscanall(cross, multicore=TRUE, n.clusters = 1,batchsize=10,cofactors=NULL, ...) </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>multicore</code></td> <td> <p> Use multiple cores (only if the package SNOW is available, otherwise this setting will be ignored) </p> </td></tr> <tr valign="top"><td><code>n.clusters</code></td> <td> <p> Number of parallel processes to spawn, recommended is setting this lower than the number of cores in the computer </p> </td></tr> <tr valign="top"><td><code>batchsize</code></td> <td> <p> Batch size. The entire set is split in jobs to reduce memory load per core. Each job contains batchsize number of traits per job. </p> </td></tr> <tr valign="top"><td><code>cofactors</code></td> <td> <p>cofactors, only used when scanfunction is mqmscan. 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></p> </td></tr></table> <p>. </p> <table summary="R argblock"> <tr valign="top"><td><code>...</code></td> <td> <p> Parameters passed through to the <code><a href="mqmscan.html">mqmscan</a></code> function used in scanning for QTLs </p> </td></tr> </table> <h3>Details</h3> <p>Uses <code>mqmscan</code> to scan for QTL's for each phenotype in the cross object. It is recomended that the package SNOW is installed before using this function on large numbers of phenotypes. </p> <h3>Value</h3> <p>Returns a MQMmulti object. This object is a list of <code><a href="scanone.html">scanone</a></code> objects that can be plotted using <code>plot.scanone(result[[trait]])</code> or using <code>mqmplot.multitrait(result)</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>References</h3> <ul> <li><p> Rossini, A., Tierney, L., and Li, N. (2003), Simple parallel statistical computing. <em>R. UW Biostatistics working paper series</em> University of Washington. <b>193</b> </p> </li> <li><p> Tierney, L., Rossini, A., Li, N., and Sevcikova, H. (2004), The snow Package: Simple Network of Workstations. Version 0.2-1. </p> </li></ul> <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> #Doing a multitrait analysis data(multitrait) multitrait <- calc.genoprob(multitrait) cof <- mqmsetcofactors(multitrait,3) multitrait <- fill.geno(multitrait) result <- mqmscanall(multitrait,cofactors=cof,batchsize=5) mqmplot.multitrait(result,"lines") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>