EVOLUTION-MANAGER
Edit File: calc.errorlod.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: Identify likely genotyping errors</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 calc.errorlod {qtl}"><tr><td>calc.errorlod {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Identify likely genotyping errors</h2> <h3>Description</h3> <p>Calculates a LOD score for each genotype, measuring the evidence for genotyping errors. </p> <h3>Usage</h3> <pre> calc.errorlod(cross, error.prob=0.01, map.function=c("haldane","kosambi","c-f","morgan"), version=c("new","old")) </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>error.prob</code></td> <td> <p>Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype)</p> </td></tr> <tr valign="top"><td><code>map.function</code></td> <td> <p>Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions.</p> </td></tr> <tr valign="top"><td><code>version</code></td> <td> <p>Specifies whether to use the original version of this function or the current (preferred) version.</p> </td></tr> </table> <h3>Details</h3> <p>Calculates, for each individual at each marker, a LOD score measuring the strength of evidence for a genotyping error, as described by Lincoln and Lander (1992). </p> <p>In the latest version, evidence for a genotype being in error is considered assuming that all other genotypes (for that individual, on that chromosome) are correct. The argument <code>version</code> allows one to specify whether this new version is used, or whether the original (old) version of the calculation is performed. </p> <p>Note that values below 4 are generally not interesting. Also note that if markers are extremely tightly linked, <em>recombination events</em> can give large error LOD scores. The error LOD scores should not be trusted blindly, but should be viewed as a tool for identifying genotypes deserving further study. </p> <p>Use <code><a href="top.errorlod.html">top.errorlod</a></code> to print all genotypes with error LOD scores above a specified threshold, <code><a href="plot.errorlod.html">plotErrorlod</a></code> to plot the error LOD scores for specified chromosomes, and <code><a href="plot.geno.html">plotGeno</a></code> to view the observed genotype data with likely errors flagged. </p> <h3>Value</h3> <p>The input <code>cross</code> object is returned with a component, <code>errorlod</code>, added to each component of <code>cross$geno</code>. The <code>errorlod</code> component is a matrix of size (n.ind x n.mar). An attribute <code>"error.prob"</code> is set to the value of the corresponding argument, for later reference. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a> </p> <h3>References</h3> <p>Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. <em>Genomics</em> <b>14</b>, 604–610. </p> <h3>See Also</h3> <p><code><a href="plot.errorlod.html">plotErrorlod</a></code>, <code><a href="top.errorlod.html">top.errorlod</a></code>, <code><a href="cleanGeno.html">cleanGeno</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.errorlod(hyper,error.prob=0.01) # print those above a specified cutoff top.errorlod(hyper, cutoff=4) # plot genotype data, flagging genotypes with error LOD > cutoff plotGeno(hyper, chr=1, ind=160:200, cutoff=7, min.sep=2) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>