EVOLUTION-MANAGER
Edit File: pull.rf.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: Pull out recombination fractions or LOD scores from a 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 pull.rf {qtl}"><tr><td>pull.rf {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Pull out recombination fractions or LOD scores from a cross object</h2> <h3>Description</h3> <p>Pull out either the pairwise recombination fractions or the LOD scores, as calculated by <code><a href="est.rf.html">est.rf</a></code>, from a cross object. </p> <h3>Usage</h3> <pre>pull.rf(cross, what=c("rf", "lod"), chr)</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>what</code></td> <td> <p>Indicates whether to pull out a matrix of estimated recombination fractions or a matrix of LOD scores.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding <code>-</code> to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.</p> </td></tr> </table> <h3>Value</h3> <p>An object of class <code>"rfmatrix"</code>, which is a matrix of either estimated recombination fractions between all marker pairs or of LOD scores (for the test of rf=1/2) for all marker pairs. </p> <p>The genetic map is included as an attribute. </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="plot.rfmatrix.html">plot.rfmatrix</a></code>, <code><a href="plot.rf.html">plotRF</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) fake.f2 <- est.rf(fake.f2) rf <- pull.rf(fake.f2) lod <- pull.rf(fake.f2, "lod") plot(rf[1,], lod[1,], xlab="rec frac", ylab="LOD score") marker <- markernames(fake.f2, chr=5)[6] par(mfrow=c(2,1)) plot(rf, marker, bandcol="gray70") plot(lod, marker, bandcol="gray70") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>