EVOLUTION-MANAGER
Edit File: fake.4way.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: Simulated data for a 4-way cross</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 fake.4way {qtl}"><tr><td>fake.4way {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Simulated data for a 4-way cross</h2> <h3>Description</h3> <p>Simulated data for a phase-known 4-way cross, obtained using <code><a href="sim.cross.html">sim.cross</a></code>. </p> <h3>Usage</h3> <pre>data(fake.4way)</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 individuals typed at 157 markers, including 8 on the X chromosome. </p> <p>There are two phenotypes (including sex, for which 0=female and 1=male). The quantitative phenotype is affected by three QTLs: two on chromosome 2 at positions 10 and 25 cM on the female genetic map, and one on chromosome 7 at position 40 cM on the female map. </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="fake.bc.html">fake.bc</a></code>, <code><a href="fake.f2.html">fake.f2</a></code>, <code><a href="listeria.html">listeria</a></code>, <code><a href="hyper.html">hyper</a></code>, <code><a href="bristle3.html">bristle3</a></code>, <code><a href="bristleX.html">bristleX</a></code> </p> <h3>Examples</h3> <pre> data(fake.4way) plot(fake.4way) summary(fake.4way) # estimate recombination fractions fake.4way <- est.rf(fake.4way) plotRF(fake.4way) # estimate genetic maps ssmap <- est.map(fake.4way, verbose=TRUE) samap <- est.map(fake.4way, sex.sp=FALSE, verbose=TRUE) plot(ssmap, samap) # error lod scores fake.4way <- calc.genoprob(fake.4way, err=0.01) fake.4way <- calc.errorlod(fake.4way, err=0.01) top.errorlod(fake.4way, cutoff=2.5) # genome scan fake.4way <- calc.genoprob(fake.4way, step=2.5) out.hk <- scanone(fake.4way, method="hk") out.em <- scanone(fake.4way, method="em") plot(out.em,out.hk,chr=c(2,7)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>