EVOLUTION-MANAGER
Edit File: sim.map.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: Simulate a genetic map</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 sim.map {qtl}"><tr><td>sim.map {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Simulate a genetic map</h2> <h3>Description</h3> <p>Simulate the positions of markers on a genetic map. </p> <h3>Usage</h3> <pre> sim.map(len=rep(100,20), n.mar=10, anchor.tel=TRUE, include.x=TRUE, sex.sp=FALSE, eq.spacing=FALSE) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>len</code></td> <td> <p>A vector specifying the chromosome lengths (in cM)</p> </td></tr> <tr valign="top"><td><code>n.mar</code></td> <td> <p>A vector specifying the number of markers per chromosome.</p> </td></tr> <tr valign="top"><td><code>anchor.tel</code></td> <td> <p>If true, markers at the two telomeres will always be included, so if <code>n.mar</code> = 1 or 2, we'll give just the two telomeric markers.</p> </td></tr> <tr valign="top"><td><code>include.x</code></td> <td> <p>Indicates whether the last chromosome should be considered the X chromosome.</p> </td></tr> <tr valign="top"><td><code>sex.sp</code></td> <td> <p>Indicates whether to create sex-specific maps, in which case the output will be a vector of 2-row matrices, with rows corresponding to the maps for the two sexes.</p> </td></tr> <tr valign="top"><td><code>eq.spacing</code></td> <td> <p>If TRUE, markers will be equally spaced.</p> </td></tr> </table> <h3>Details</h3> <p>Aside from the telomeric markers, marker positions are simulated as iid Uniform(<i>0,L</i>). If <code>len</code> or <code>n.mar</code> has just one element, it is expanded to the length of the other argument. If they both have just one element, only one chromosome is simulated. </p> <p>If <code>eq.spacing</code> is TRUE, markers are equally spaced between 0 and <i>L</i>. If <code>anchor.tel</code> is FALSE, telomeric markers are not included. </p> <h3>Value</h3> <p>A list of vectors, each specifying the locations of the markers. Each component of the list is given class <code>A</code> or <code>X</code>, according to whether it is autosomal or the X chromosome. </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="sim.cross.html">sim.cross</a></code>, <code><a href="plot.map.html">plotMap</a></code>, <code><a href="replace.map.html">replace.map</a></code>, <code><a href="pull.map.html">pull.map</a></code> </p> <h3>Examples</h3> <pre> # simulate 4 autosomes, each with 10 markers map <- sim.map(c(100,90,80,40), 10, include.x=FALSE) plotMap(map) # equally spaced markers map2 <- sim.map(c(100,90,80,40), 10, include.x=FALSE, eq.spacing=TRUE) plot(map2) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>