EVOLUTION-MANAGER
Edit File: subset.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: Subsetting two-dimensional permutation test 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 subset.scantwoperm {qtl}"><tr><td>subset.scantwoperm {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Subsetting two-dimensional permutation test results</h2> <h3>Description</h3> <p>Pull out results for a specified set LOD columns from permutation results from <code><a href="scantwo.html">scantwo</a></code>. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scantwoperm' subset(x, repl, lodcolumn, ...) ## S3 method for class 'scantwoperm' x[repl, lodcolumn] </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>Permutation results from <code><a href="scantwo.html">scantwo</a></code>, run with <code>n.perm</code>>0.</p> </td></tr> <tr valign="top"><td><code>repl</code></td> <td> <p>A vector specifying which permutation replicates to keep or (if negative) omit. Ignored in case of X-chr specific permutations</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>scantwo</code> permutation results, 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.scantwoperm.html">summary.scantwoperm</a></code>, <code><a href="scantwo.html">scantwo</a></code>, <code><a href="c.scantwoperm.html">c.scantwoperm</a></code>, <code><a href="c.scantwoperm.html">rbind.scantwoperm</a></code> </p> <h3>Examples</h3> <pre> data(fake.bc) fake.bc <- calc.genoprob(fake.bc, step=0) operm <- scantwo(fake.bc, method="hk", pheno.col=1:2, n.perm=5) operm2 <- subset(operm, lodcolumn=2) # alternatively operm2alt <- operm[,2] </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>