EVOLUTION-MANAGER
Edit File: switchAlleles.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: Switch alleles at selected 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 switchAlleles {qtl}"><tr><td>switchAlleles {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Switch alleles at selected markers</h2> <h3>Description</h3> <p>Switch alleles at selected markers in a cross object. </p> <h3>Usage</h3> <pre>switchAlleles(cross, markers, switch=c("AB", "CD", "ABCD", "parents"))</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>markers</code></td> <td> <p>Names of markers whose alleles are to be switched.</p> </td></tr> <tr valign="top"><td><code>switch</code></td> <td> <p>For a 4-way cross, indicates how to switch the alleles (A for B, C for D, both A for B and C for D), or both A for C and B for D (<code>parents</code>).</p> </td></tr> </table> <h3>Details</h3> <p>For a backcross, we exchange homozygotes (AA) and heterozygotes (AB). </p> <p>For doubled haploids and recombinant inbred lines, we exchange the two homozygotes. </p> <p>For an intercross, we exchange the two homozygotes, and exchange C (i.e., not AA) and D (i.e., not BB). (The heterozygotes in an intercross are left unchanged.) </p> <p>For a 4-way cross, we consider the argument <code>switch</code>, and the exchanges among the genotypes are more complicated. </p> <h3>Value</h3> <p>The input cross object, with alleles at selected markers 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="checkAlleles.html">checkAlleles</a></code>, <code><a href="est.rf.html">est.rf</a></code>, <code><a href="geno.crosstab.html">geno.crosstab</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) geno.crosstab(fake.f2, "D5M391", "D5M81") # switch homozygotes at marker D5M391 fake.f2 <- switchAlleles(fake.f2, "D5M391") geno.crosstab(fake.f2, "D5M391", "D5M81") ## Not run: fake.f2 <- est.rf(fake.f2) checkAlleles(fake.f2) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>