EVOLUTION-MANAGER
Edit File: find.pseudomarker.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: Find the pseudomarker closest to a specified position</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 find.pseudomarker {qtl}"><tr><td>find.pseudomarker {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Find the pseudomarker closest to a specified position</h2> <h3>Description</h3> <p>Find the pseudomarker closest to a specified position on a chromosome. </p> <h3>Usage</h3> <pre>find.pseudomarker(cross, chr, pos, where=c("draws", "prob"), addchr=TRUE)</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> <tr valign="top"><td><code>chr</code></td> <td> <p>A vector of chromosome identifiers, or a single such.</p> </td></tr> <tr valign="top"><td><code>pos</code></td> <td> <p>A vector of cM positions.</p> </td></tr> <tr valign="top"><td><code>where</code></td> <td> <p>Indicates whether to look in the <code>draws</code> or <code>prob</code> components of the input cross.</p> </td></tr> <tr valign="top"><td><code>addchr</code></td> <td> <p>If TRUE, include something like <code>"c5."</code> at the beginning of the names of non-pseudomarker locations, as in the output of <code><a href="scanone.html">scanone</a></code>; if FALSE, don't include this sort of string, as in the genotype probabilities from <code><a href="calc.genoprob.html">calc.genoprob</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>If the input <code>chr</code> has length one, it is expanded to the same length as the input <code>pos</code>. </p> <p>If multiple markers are exactly the same distance from the specified position, one is chosen at random from among those with the most genotype data. </p> <p>For a cross with sex-specific maps, the input positions are assumed to correspond to the female genetic map. </p> <h3>Value</h3> <p>A vector of pseudomarker names (of the same length as the input <code>pos</code>), corresponding to the markers nearest to the specified chromosomes/positions. </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="find.flanking.html">find.flanking</a></code>, <code><a href="plot.pxg.html">plotPXG</a></code>, <code><a href="effectplot.html">effectplot</a></code>, <code><a href="find.marker.html">find.marker</a></code>, <code><a href="find.markerpos.html">find.markerpos</a></code> </p> <h3>Examples</h3> <pre> data(listeria) listeria <- calc.genoprob(listeria, step=2.5) find.pseudomarker(listeria, 5, 28, "prob") find.pseudomarker(listeria, c(1, 5, 13), c(81, 28, 26), "prob") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>