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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: Maximum peak in two-dimensional genome scan</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 max.scantwo {qtl}"><tr><td>max.scantwo {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Maximum peak in two-dimensional genome scan</h2> <h3>Description</h3> <p>Print the pair of loci with the largest LOD score in the results of <code><a href="scantwo.html">scantwo</a></code>. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scantwo' max(object, lodcolumn=1, what=c("best", "full", "add", "int"), na.rm=TRUE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>object</code></td> <td> <p>An object of class <code>scantwo</code>, the output of the function <code><a href="scantwo.html">scantwo</a></code>.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>If the scantwo results contain LOD scores for multiple phenotypes, this argument indicates which to use.</p> </td></tr> <tr valign="top"><td><code>what</code></td> <td> <p>Indicates for which LOD score the maximum should be reported.</p> </td></tr> <tr valign="top"><td><code>na.rm</code></td> <td> <p>Ignored.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored.</p> </td></tr> </table> <h3>Details</h3> <p>This is very similar to the <code><a href="summary.scantwo.html">summary.scantwo</a></code> function, though this pulls out one pair of positions. </p> <p>If <code>what="best"</code>, we find the pair of positions at which the LOD score for the full model (2 QTL + interaction) is maximized, and then also print the positions on that same pair of chromosomes at which the additive LOD score is maximized. </p> <p>In the other cases, we pull out the pair of positions with the largest LOD score; which LOD score is considered is indicated by the <code>what</code> argument. </p> <h3>Value</h3> <p>An object of class <code>summary.scantwo</code>, to be printed by <code>print.summary.scantwo</code>, with the pair of positions with the maximum LOD score. (Which LOD score is considered is indicated by the <code>what</code> argument.) </p> <h3>Output of addpair</h3> <p><b>Note</b> that, for output from <code><a href="addpair.html">addpair</a></code> in which the new loci are indicated explicitly in the formula, the summary provided by <code>max.scantwo</code> is somewhat special. </p> <p>All arguments (except, of course, the input <code>object</code>) are ignored. </p> <p>If the formula is symmetric in the two new QTL, the output has just two LOD score columns: <code>lod.2v0</code> comparing the full model to the model with neither of the new QTL, and <code>lod.2v1</code> comparing the full model to the model with just one new QTL. </p> <p>If the formula is <em>not</em> symmetric in the two new QTL, the output has three LOD score columns: <code>lod.2v0</code> comparing the full model to the model with neither of the new QTL, <code>lod.2v1b</code> comparing the full model to the model in which the first of the new QTL is omitted, and <code>lod.2v1a</code> comparing the full model to the model with the second of the new QTL omitted. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a> </p> <h3>See Also</h3> <p><code><a href="scantwo.html">scantwo</a></code>, <code><a href="plot.scantwo.html">plot.scantwo</a></code>, <code><a href="summary.scantwo.html">summary.scantwo</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=10) out.2dim <- scantwo(fake.f2, method="hk") max(out.2dim) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>