EVOLUTION-MANAGER
Edit File: mqmtestnormal.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: Shapiro normality test used for 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 mqmtestnormal {qtl}"><tr><td>mqmtestnormal {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2> Shapiro normality test used for MQM </h2> <h3>Description</h3> <p>Wraps a shapiro's normality test from the nortest package. This function is used in MQM to test the normality of the trait under investigation </p> <h3>Usage</h3> <pre> mqmtestnormal(cross, pheno.col = 1,significance=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>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>significance</code></td> <td> <p>Significance level used in the normality test. Lower significance levels will accept larger deviations from normality. </p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print result as well as return it. </p> </td></tr> </table> <h3>Details</h3> <p>For augmented data (as from <code><a href="mqmaugment.html">mqmaugment</a></code>), the cross is first reduced to distinct individuals. Furthermore the shapiro used to test normality works only for 3 <= nind(cross) <= 5000 </p> <h3>Value</h3> <p>Boolean indicating normality of the trait in pheno.col. (FALSE when not normally distributed.) </p> <h3>Author(s)</h3> <p>Danny Arends <a href="mailto:danny.arends@gmail.com">danny.arends@gmail.com</a> </p> <h3>See Also</h3> <ul> <li> <p><code><a href="../../stats/html/shapiro.test.html">shapiro.test</a></code> - Function wrapped by our mqmtestnormal </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> data(multitrait) # test normality of 7th phenotype mqmtestnormal(multitrait, pheno.col=7) # take log multitrait <- transformPheno(multitrait, pheno.col=7, transf=log) # test again mqmtestnormal(multitrait, pheno.col=7) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>