EVOLUTION-MANAGER
Edit File: fake.bc.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 backcross</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.bc {qtl}"><tr><td>fake.bc {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Simulated data for a backcross</h2> <h3>Description</h3> <p>Simulated data for a backcross, obtained using <code><a href="sim.cross.html">sim.cross</a></code>. </p> <h3>Usage</h3> <pre>data(fake.bc)</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 400 backcross individuals typed at 91 markers and with two phenotypes and two covariates (sex and age). </p> <p>The two phenotypes are due to four QTLs, with no epistasis. There is one on chromosome 2 (at 30 cM), two on chromosome 5 (at 10 and 50 cM), and one on chromosome 10 (at 30 cM). The QTL on chromosome 2 has an effect only in the males (sex=1); the two QTLs on chromosome 5 have effect in coupling for the first phenotype and in repulsion for the second phenotype. Age has an effect of increasing the phenotypes. </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.4way.html">fake.4way</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.bc) summary(fake.bc) plot(fake.bc) # genome scans without covariates fake.bc <- calc.genoprob(fake.bc, step=2.5) out.nocovar <- scanone(fake.bc, pheno.col=1:2) # genome scans with covariates ac <- pull.pheno(fake.bc, c("sex","age")) ic <- pull.pheno(fake.bc, "sex") out.covar <- scanone(fake.bc, pheno.col=1:2, addcovar=ac, intcovar=ic) # summaries summary(out.nocovar, thr=3, format="allpeaks") summary(out.covar, thr=3, format="allpeaks") # plots plot(out.nocovar, out.covar, chr=c(2,5,10), lod=1, col="blue", lty=1:2, ylim=c(0,13)) plot(out.nocovar, out.covar, chr=c(2,5,10), lod=2, col="red", lty=1:2, add=TRUE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>