EVOLUTION-MANAGER
Edit File: cleanGeno.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: Delete genotypes that are possibly in error</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 cleanGeno {qtl}"><tr><td>cleanGeno {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Delete genotypes that are possibly in error</h2> <h3>Description</h3> <p>Delete genotypes from a cross that are indicated to be possibly in error, as they result in apparent tight double-crossovers. </p> <h3>Usage</h3> <pre> cleanGeno(cross, chr, maxdist=2.5, maxmark=2, verbose=TRUE) </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>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> <tr valign="top"><td><code>maxdist</code></td> <td> <p>A vector specifying the maximum distance between two crossovers.</p> </td></tr> <tr valign="top"><td><code>maxmark</code></td> <td> <p>A vector specifying the maximum number of typed markers between two crossovers.</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print information on the numbers of genotypes omitted from each chromosome.</p> </td></tr> </table> <h3>Details</h3> <p>We first use <code><a href="locateXO.html">locateXO</a></code> to identify crossover locations. If a pair of adjacted crossovers are separated by no more than <code>maxdist</code> and contain no more than <code>maxmark</code> genotyped markers, the intervening genotypes are omitted (that is, changed to <code>NA</code>). </p> <p>The arguments <code>maxdist</code> and <code>maxmark</code> may be vectors. (If both have length greater than 1, they must have the same length.) If they are vectors, genotypes are omitted if they satisify any one of the (<code>maxdist</code>, <code>maxmark</code>) pairs. </p> <h3>Value</h3> <p>The input <code>cross</code> object with suspect genotypes omitted. </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="locateXO.html">locateXO</a></code>, <code><a href="countXO.html">countXO</a></code>, <code><a href="calc.errorlod.html">calc.errorlod</a></code> </p> <h3>Examples</h3> <pre> data(hyper) sum(ntyped(hyper)) hyperc <- cleanGeno(hyper, chr=4, maxdist=c(2.5, 10), maxmark=c(2, 1)) sum(ntyped(hyperc)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>