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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: Estimate QTL LOD score significance using permutations or...</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 mqmpermutation {qtl}"><tr><td>mqmpermutation {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Estimate QTL LOD score significance using permutations or simulations </h2> <h3>Description</h3> <p>Two randomization approaches to obtain estimates of QTL significance: </p> <ul> <li><p> Random redistribution of traits (method='permutation') </p> </li> <li><p> Random redistribution of simulated trait values (method='simulation') </p> </li></ul> <p>Calculations can be parallelized using the SNOW package. </p> <h3>Usage</h3> <pre> mqmpermutation(cross, scanfunction=scanone, pheno.col=1, multicore=TRUE, n.perm=10, file="MQM_output.txt", n.cluster=1, method=c("permutation","simulation"), cofactors=NULL, plot=FALSE, 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>scanfunction</code></td> <td> <p> Function to use when mappingQTL's (either scanone,cim or mqm)</p> </td></tr> <tr valign="top"><td><code>pheno.col</code></td> <td> <p>Column number in the phenotype matrix which should be used as the phenotype. This can be a vector of integers. </p> </td></tr> <tr valign="top"><td><code>multicore</code></td> <td> <p> Use multicore (if available)</p> </td></tr> <tr valign="top"><td><code>n.perm</code></td> <td> <p> Number of permutations to perform (DEFAULT=10, should be 1000, or higher, for publications) </p> </td></tr> <tr valign="top"><td><code>file</code></td> <td> <p> Name of the intermediate output file used </p> </td></tr> <tr valign="top"><td><code>n.cluster</code></td> <td> <p> Number of child processes to split the job into </p> </td></tr> <tr valign="top"><td><code>method</code></td> <td> <p> What kind permutation should occur: permutation or simulation </p> </td></tr> <tr valign="top"><td><code>cofactors</code></td> <td> <p>cofactors, only used when scanfunction is mqm. 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>plot</code></td> <td> <p>If TRUE, make a plot</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print tracing information</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Parameters passed through to the <code><a href="scanone.html">scanone</a></code>, <code><a href="cim.html">cim</a></code> or <code><a href="mqmscan.html">mqmscan</a></code> functions</p> </td></tr> </table> <h3>Details</h3> <p>Analysis of <code><a href="scanone.html">scanone</a></code>, <code><a href="cim.html">cim</a></code> or <code><a href="mqmscan.html">mqmscan</a></code> to scan for QTL in shuffled/randomized data. It is recommended to also install the <code>snow</code> library. The <code>snow</code> library allows calculations to run on multiple cores or even scale it up to an entire cluster, thus speeding up calculation. </p> <h3>Value</h3> <p>Returns a mqmmulti object. this object is a list of scanone objects that can be plotted using <code>plot.scanone(result[[trait]])</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> Bruno M. Tesson, Ritsert C. Jansen (2009) Chapter 3.7. Determining the significance threshold <em>eQTL Analysis in Mice and Rats</em> <b>1</b>, 20–25 </p> </li> <li><p> Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. <em>Genetics</em> <b>138</b>, 963–971. </p> </li> <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> # Use the multitrait dataset data(multitrait) multitrait <- calc.genoprob(multitrait) result <- mqmpermutation(multitrait,pheno.col=7, n.perm=2, batchsize=2) ## Not run: #Set 50 cofactors cof <- mqmautocofactors(multitrait,50) ## End(Not run) multitrait <- fill.geno(multitrait) result <- mqmpermutation(multitrait,scanfunction=mqmscan,cofactors=cof, pheno.col=7, n.perm=2,batchsize=2,verbose=FALSE) #Create a permutation object f2perm <- mqmprocesspermutation(result) #Get Significant LOD thresholds 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>