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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: Permutation test for mean effect in scanonevar</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 scanonevar.meanperm {qtl}"><tr><td>scanonevar.meanperm {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Permutation test for mean effect in scanonevar</h2> <h3>Description</h3> <p>Executes permutations of the genotypes in the mean-effect part of scanonevar</p> <h3>Usage</h3> <pre> scanonevar.meanperm(cross, pheno.col=1, mean_covar=NULL, var_covar=NULL, maxit=25, tol=1e-6, n.mean.perm = 2, seed = 27517, quiet=TRUE) </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 must be a single value (integer index or phenotype name) or a numeric vector of phenotype values, in which case it must have the length equal to the number of individuals in the cross, and there must be either non-integers or values < 1 or > no. phenotypes; this last case may be useful for studying transformations.</p> </td></tr> <tr valign="top"><td><code>mean_covar</code></td> <td> <p>Numeric matrix with covariates affecting the mean.</p> </td></tr> <tr valign="top"><td><code>var_covar</code></td> <td> <p>Numeric matrix with covariates affecting the variances.</p> </td></tr> <tr valign="top"><td><code>maxit</code></td> <td> <p>Maximum number of iterations in the algorithm to fit the model at a given position.</p> </td></tr> <tr valign="top"><td><code>tol</code></td> <td> <p>Tolerance for convergence.</p> </td></tr> <tr valign="top"><td><code>n.mean.perm</code></td> <td> <p>Numeric vector of length one indicates the number of permutations to execute.</p> </td></tr> <tr valign="top"><td><code>seed</code></td> <td> <p>Numeric vector of length one indicates the random seed to start the permutations.</p> </td></tr> <tr valign="top"><td><code>quiet</code></td> <td> <p>If <code>FALSE</code>, print some information about the course of the calculations.</p> </td></tr> </table> <h3>Value</h3> <p>A vector of length <code>n.mean.perm</code> of the maximum negative log10 p-value that resulted from each permutation. </p> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>