EVOLUTION-MANAGER
Edit File: subset.scanone.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: Subsetting the results of a 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 subset.scanone {qtl}"><tr><td>subset.scanone {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Subsetting the results of a genome scan</h2> <h3>Description</h3> <p>Pull out a specified set of chromosomes and/or LOD columns from <code><a href="scanone.html">scanone</a></code> output. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanone' subset(x, chr, lodcolumn, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>scanone</code>, output from <code><a href="scanone.html">scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector specifying which chromosomes to keep. 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>A vector specifying which LOD columns to keep (or, if negative), omit. These should be between 1 and the number of LOD columns in the input <code>x</code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Value</h3> <p>The input <code>scanone</code> object, but with only the specified subset of the data.</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="summary.scanone.html">summary.scanone</a></code>, <code><a href="scanone.html">scanone</a></code> </p> <h3>Examples</h3> <pre> data(fake.bc) fake.bc <- calc.genoprob(fake.bc, step=2.5) out <- scanone(fake.bc, method="hk", pheno.col=1:2) summary(subset(out, chr=18:19), format="allpeaks") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>