EVOLUTION-MANAGER
Edit File: summary.scantwoperm.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: LOD thresholds from scantwo permutation results</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 summary.scantwoperm {qtl}"><tr><td>summary.scantwoperm {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>LOD thresholds from scantwo permutation results</h2> <h3>Description</h3> <p>Print the estimated genome-wide LOD thresholds on the basis of permutation results from <code><a href="scantwo.html">scantwo</a></code> (with <code>n.perm</code> > 0). </p> <h3>Usage</h3> <pre> ## S3 method for class 'scantwoperm' summary(object, alpha=c(0.05, 0.10), ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>object</code></td> <td> <p>Output from the function <code><a href="scantwo.html">scantwo</a></code> with <code>n.perm</code> > 0.</p> </td></tr> <tr valign="top"><td><code>alpha</code></td> <td> <p>Genome-wide significance levels.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Details</h3> <p>We take the <i>1-alpha</i> quantiles of the individual LOD scores. </p> <p>In the case of X-chr-specific permutations, we use the combined length of the autosomes, <i>L_A</i>, and the length of the X chromosome, <i>L_X</i>, and calculate the area of the A:A, A:X, and X:X regions as <i>L_A^2/2</i>, <i>L_A L_X</i>, and <i>L_X^2/2</i>, and then use the nominal significance levels of <i>1 - (1-alpha)^p</i>, where <i>p</i> is the proportional area for that region. </p> <h3>Value</h3> <p>An object of class <code>summary.scantwoperm</code>, to be printed by <code>print.summary.scantwoperm</code>. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a></p> <h3>References</h3> <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> <h3>See Also</h3> <p><code><a href="scantwo.html">scantwo</a></code>, <code><a href="summary.scantwo.html">summary.scantwo</a></code>, <code><a href="plot.scantwoperm.html">plot.scantwoperm</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=0) ## Not run: operm <- scantwo(fake.f2, n.perm=100, method="hk") summary(operm) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>