EVOLUTION-MANAGER
Edit File: badorder.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: An intercross with misplaced markers</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 badorder {qtl}"><tr><td>badorder {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>An intercross with misplaced markers</h2> <h3>Description</h3> <p>Simulated data for an intercross with some markers out of order. </p> <h3>Usage</h3> <pre>data(badorder)</pre> <h3>Format</h3> <p>An object of class <code>cross</code>. See <code><a href="read.cross.html">read.cross</a></code> for details. </p> <h3>Details</h3> <p>There are 250 F2 individuals typed at a total of 36 markers on four chromosomes. The data were simulated with QTLs at the center of chromosomes 1 and 3. </p> <p>The order of several markers on chromosome 1 is incorrect. Markers on chromosomes 2 and 3 are switched. </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="est.rf.html">est.rf</a></code>, <code><a href="ripple.html">ripple</a></code>, <code><a href="est.map.html">est.map</a></code>, <code><a href="sim.cross.html">sim.cross</a></code> </p> <h3>Examples</h3> <pre> data(badorder) # estimate recombination fractions badorder <- est.rf(badorder) plotRF(badorder) # re-estimate map newmap <- est.map(badorder) plotMap(badorder, newmap) # assess marker order on chr 1 rip3 <- ripple(badorder, chr=1, window=3) summary(rip3) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>