EVOLUTION-MANAGER
Edit File: fill.geno.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: Fill holes in genotype data</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 fill.geno {qtl}"><tr><td>fill.geno {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Fill holes in genotype data</h2> <h3>Description</h3> <p>Replace the genotype data for a cross with a version imputed either by simulation with <code><a href="sim.geno.html">sim.geno</a></code>, by the Viterbi algorithm with <code><a href="argmax.geno.html">argmax.geno</a></code>, or simply filling in genotypes between markers that have matching genotypes. </p> <h3>Usage</h3> <pre> fill.geno(cross, method=c("imp","argmax", "no_dbl_XO", "maxmarginal"), error.prob=0.0001, map.function=c("haldane","kosambi","c-f","morgan"), min.prob=0.95) </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>method</code></td> <td> <p>Indicates whether to impute using a single simulation replicate from <code><a href="sim.geno.html">sim.geno</a></code>, using the Viterbi algorithm, as implemented in <code><a href="argmax.geno.html">argmax.geno</a></code>, by simply filling in missing genotypes between markers with matching genotypes, or by choosing (at each marker) the genotype with maximal marginal probability.</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 or Carter-Falconer map function when converting genetic distances into recombination fractions.</p> </td></tr> <tr valign="top"><td><code>min.prob</code></td> <td> <p>For <code>method="maxmarginal"</code>, genotypes with probability greater than this value will be imputed; those less than this value will be made missing.</p> </td></tr> </table> <h3>Details</h3> <p>This function is written so that one may perform rough genome scans by marker regression without having to drop individuals with missing genotype data. <b>We must caution the user that little trust should be placed in the results</b>. </p> <p>With <code>method="imp"</code>, a single random imputation is performed, using <code><a href="sim.geno.html">sim.geno</a></code>. </p> <p>With <code>method="argmax"</code>, for each individual the most probable sequence of genotypes, given the observed data (via <code>argmax.geno</code>), is used. </p> <p>With <code>method="no_dbl_XO"</code>, non-recombinant intervals are filled in; recombinant intervals are left missing. For example, a sequence of genotypes like <code>A---A---H---H---A</code> (with <code>A</code> and <code>H</code> corresponding to genotypes AA and AB, respectively, and with <code>-</code> being a missing value) will be filled in as <code>AAAAA---HHHHH---A</code>. </p> <p>With <code>method="maxmarginal"</code>, the conditional genotype probabilities are calculated with <code>calc.genoprob</code>, and then at each marker, the most probable genotype is determined. This is taken as the imputed genotype if it has probability greater than <code>min.prob</code>; otherwise it is made missing. </p> <p>With <code>method="no_dbl_XO"</code> and <code>method="maxmarginal"</code>, some missing genotypes likely remain. With <code>method="maxmarginal"</code>, some observed genotypes may be made missing. </p> <h3>Value</h3> <p>The input <code>cross</code> object with the genotype data replaced by an imputed version. Any intermediate calculations (such as is produced by <code><a href="calc.genoprob.html">calc.genoprob</a></code>, <code><a href="argmax.geno.html">argmax.geno</a></code> and <code><a href="sim.geno.html">sim.geno</a></code>) are removed. </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="sim.geno.html">sim.geno</a></code>, <code><a href="argmax.geno.html">argmax.geno</a></code> </p> <h3>Examples</h3> <pre> data(hyper) out.mr <- scantwo(fill.geno(hyper,method="argmax"), method="mr") plot(out.mr) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>