EVOLUTION-MANAGER
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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 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.scanone {qtl}"><tr><td>max.scanone {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Maximum peak in genome scan</h2> <h3>Description</h3> <p>Print the row of the output from <code><a href="scanone.html">scanone</a></code> that corresponds to the maximum LOD, genome-wide. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanone' max(object, chr, lodcolumn=1, na.rm=TRUE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>object</code></td> <td> <p>An object of the form output by the function <code><a href="scanone.html">scanone</a></code>: a data.frame whose third column is the LOD score.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding <code>-</code> to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>An integer, indicating which of the LOD score columns should be considered in pulling out the peak (these are indexed 1, 2, ...).</p> </td></tr> <tr valign="top"><td><code>na.rm</code></td> <td> <p>A logical indicating whether missing values should be removed.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored.</p> </td></tr> </table> <h3>Value</h3> <p>An object of class <code>summary.scanone</code>, to be printed by <code>print.summary.scanone</code>. This is a data.frame with one row, corresponding to the maximum LOD peak either genome-wide or for the particular chromosome specified. </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="scanone.html">scanone</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code>, <code><a href="summary.scanone.html">summary.scanone</a></code> </p> <h3>Examples</h3> <pre> data(listeria) listeria <- calc.genoprob(listeria, step=2.5) out <- scanone(listeria, model="2part", upper=TRUE) # Maximum peak for LOD(p,mu) max(out) # Maximum peak for LOD(p,mu) on chr 5 max(out,chr=5) # Maximum peak for LOD(p,mu) on chromosomes other than chr 13 max(out,chr="-13") # Maximum peak for LOD(p) max(out, lodcolumn=2) # Maximum peak for LOD(mu) max(out, lodcolumn=3) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>