EVOLUTION-MANAGER
Edit File: arithscan.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: Arithmetic operators for scanone and scantwo 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 arithscan {qtl}"><tr><td>arithscan {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Arithmetic operators for scanone and scantwo results</h2> <h3>Description</h3> <p>Add or subtract LOD scores in results from <code><a href="scanone.html">scanone</a></code> or <code><a href="scantwo.html">scantwo</a></code>. </p> <h3>Usage</h3> <pre> scan1+scan2 scan1-scan2 </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>scan1, scan2</code></td> <td> <p>Genome scan results on the same set of chromosomes and markers, as output by <code><a href="scanone.html">scanone</a></code> or <code><a href="scantwo.html">scantwo</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>This is used to calculate the sum or difference of LOD scores of two genome scan results. It is particularly useful for calculating the LOD scores for QTL-by-covariate interactions (see the example, below). Note that the degrees of freedom are also added or subtracted. </p> <h3>Value</h3> <p>The same type of 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") # scan with additive but not the interactive covariate out.acovar <- scanone(fake.bc, addcovar=ac) # scan with interactive covariate out.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic) # plot the difference of with and without the interactive covariate # This is a LOD score for a test of QTL x covariate interaction plot(out.icovar-out.acovar) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>