EVOLUTION-MANAGER
Edit File: formLinkageGroups.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: Partition markers into linkage groups</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 formLinkageGroups {qtl}"><tr><td>formLinkageGroups {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Partition markers into linkage groups</h2> <h3>Description</h3> <p>Use pairwise linkage information between markers (as calculated by <code><a href="est.rf.html">est.rf</a></code> to partition markers into linkage groups. </p> <h3>Usage</h3> <pre> formLinkageGroups(cross, max.rf=0.25, min.lod=3, reorgMarkers=FALSE, verbose=FALSE) </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>max.rf</code></td> <td> <p>Maximum recombination fraction for placing two markers in the same linkage group (see Details).</p> </td></tr> <tr valign="top"><td><code>min.lod</code></td> <td> <p>Minimum LOD score for placing two markers in the same linkage group (see Details).</p> </td></tr> <tr valign="top"><td><code>reorgMarkers</code></td> <td> <p>If TRUE, the output is a cross object, like the input, but with the markers organized into the inferred linkage groups. If FALSE, the output is a table indicating the initial chromosome assignments and the inferred linkage group partitions.</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, display information about the progress of the calculations.</p> </td></tr> </table> <h3>Details</h3> <p>Two markers are placed in the same linkage group if the estimated recombination fraction between them is <i><=</i> <code>max.rf</code> and the LOD score (for the test of the rec. frac. = 1/2) is <i>>=</i> <code>min.lod</code>. The transitive property (if A is linked to B and B is linked to C then A is linked to C) is used to close the groups. </p> <h3>Value</h3> <p>If <code>reorgMarkers=FALSE</code> (the default), the output is a data frame with rows corresponding to the markers and with two columns: the initial chromosome assignment and the inferred linkage group. Linkage groups are ordered by the number of markers they contain (from largest to smallest). </p> <p>If <code>reorgMarkers=TRUE</code>, the output is a cross object, like the input, but with the markers reorganized into the inferred linkage groups. The marker order and marker positions within the linkage groups are arbitrary. </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="orderMarkers.html">orderMarkers</a></code> </p> <h3>Examples</h3> <pre> data(listeria) listeria <- est.rf(listeria) result <- formLinkageGroups(listeria) tab <- table(result[,1], result[,2]) apply(tab, 1, function(a) sum(a!=0)) apply(tab, 2, function(a) sum(a!=0)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>