EVOLUTION-MANAGER
Edit File: top.errorlod.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: List genotypes with large error LOD scores</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 top.errorlod {qtl}"><tr><td>top.errorlod {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>List genotypes with large error LOD scores</h2> <h3>Description</h3> <p>Prints those genotypes with error LOD scores above a specified cutoff. </p> <h3>Usage</h3> <pre> top.errorlod(cross, chr, cutoff=4, msg=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>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>cutoff</code></td> <td> <p>Only those genotypes with error LOD scores above this cutoff will be listed.</p> </td></tr> <tr valign="top"><td><code>msg</code></td> <td> <p>If TRUE, print a message if there are no apparent errors.</p> </td></tr> </table> <h3>Value</h3> <p>A data.frame with 4 columns, whose rows correspond to the genotypes that are possibly in error. The four columns give the chromosome number, individual number, marker name, and error LOD score. </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="calc.errorlod.html">calc.errorlod</a></code>, <code><a href="plot.geno.html">plotGeno</a></code>, <code><a href="plot.errorlod.html">plotErrorlod</a></code> </p> <h3>Examples</h3> <pre> data(hyper) # Calculate error LOD scores hyper <- calc.errorlod(hyper,error.prob=0.01) # Print those above a specified cutoff top.errorlod(hyper,cutoff=4) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>