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: Arithmetic Operators for permutation 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 arithscanperm {qtl}"><tr><td>arithscanperm {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Arithmetic Operators for permutation results</h2> <h3>Description</h3> <p>Add or subtract LOD scores in permutation results from <code><a href="scanone.html">scanone</a></code> or <code><a href="scantwo.html">scantwo</a></code>. </p> <h3>Usage</h3> <pre> perm1+perm2 perm1-perm2 </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>perm1, perm2</code></td> <td> <p>Permutation results from <code><a href="scanone.html">scanone</a></code> or <code><a href="scantwo.html">scantwo</a></code>, on the same set of chromosomes and markers.</p> </td></tr> </table> <h3>Details</h3> <p>This is used to calculate the sum or difference of LOD scores of two sets of permutation results from <code><a href="scanone.html">scanone</a></code> or <code><a href="scantwo.html">scantwo</a></code>. One must be careful to ensure that the permutations are perfectly linked, which will require the use of <code><a href="../../base/html/Random.html">set.seed</a></code>. </p> <h3>Value</h3> <p>The same data structure as the input objects, with LOD scores added or subtracted. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a></p> <h3>Examples</h3> <pre> data(fake.bc) fake.bc <- calc.genoprob(fake.bc, step=2.5) # covariates ac <- pull.pheno(fake.bc, c("sex","age")) ic <- pull.pheno(fake.bc, "sex") # set seed theseed <- round(runif(1, 1, 10^8)) set.seed(theseed) # permutations with additive but not the interactive covariate ## Not run: operm.acovar <- scanone(fake.bc, addcovar=ac, n.perm=1000) # re-set the seed set.seed(theseed) # permutations with interactive covariate ## Not run: operm.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic, n.perm=1000) ## End(Not run) # permutation results for the QTL x covariate interaction operm.gxc <- operm.icovar - operm.acovar # LOD thresholds summary(operm.gxc) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>