EVOLUTION-MANAGER
Edit File: reduce2grid.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: Reduce to a grid of pseudomarkers.</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 reduce2grid {qtl}"><tr><td>reduce2grid {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Reduce to a grid of pseudomarkers.</h2> <h3>Description</h3> <p>For high-density marker data, rather than run <code><a href="scanone.html">scanone</a></code> at both the markers and at a set of pseudomarkers, we reduce to just a set of evenly-spaced pseudomarkers </p> <h3>Usage</h3> <pre> reduce2grid(cross) </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> </table> <h3>Details</h3> <p>Genotype probabilities (from <code><a href="calc.genoprob.html">calc.genoprob</a></code>) and/or imputations (from <code><a href="sim.geno.html">sim.geno</a></code>) are subset to a grid of pseudomarkers. </p> <p>This is so that, in the case of high-density markers, we can do the genome scan calculations at a smaller set of points (on an evenly-spaced grid, but not at the markers) to save computation time. </p> <p>You need to first have run <code><a href="calc.genoprob.html">calc.genoprob</a></code> and/or <code><a href="sim.geno.html">sim.geno</a></code>, and you must use <code>stepwidth="fixed"</code>. </p> <p>When plotting results with <code><a href="plot.scanone.html">plot.scanone</a></code>, use <code>incl.markers=FALSE</code>, as the output of <code><a href="scanone.html">scanone</a></code> won't include information about the marker locations and so will plot tick marks only at the first marker on each chromosome. </p> <h3>Value</h3> <p>The input <code>cross</code> object with included genotype probabilities or imputations subset to an evenly-spaced grid. </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.genoprob.html">calc.genoprob</a></code>, <code><a href="sim.geno.html">sim.geno</a></code>, <code><a href="scanone.html">scanone</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper, step=2) hypersub <- reduce2grid(hyper) ## Not run: out <- scanone(hypersub) plot(out, incl.markers=FALSE) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>