EVOLUTION-MANAGER
Edit File: pull.genoprob.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 the genotype probabilities 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.genoprob {qtl}"><tr><td>pull.genoprob {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Pull out the genotype probabilities from a cross</h2> <h3>Description</h3> <p>Pull out the results of <code><a href="calc.genoprob.html">calc.genoprob</a></code> from a cross as a matrix. </p> <h3>Usage</h3> <pre>pull.genoprob(cross, chr, omit.first.prob=FALSE, include.pos.info=FALSE, rotate=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>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>omit.first.prob</code></td> <td> <p>If TRUE, omit the probabilities for the first genotype at each position (since they sum to 1).</p> </td></tr> <tr valign="top"><td><code>include.pos.info</code></td> <td> <p>If TRUE, include columns with marker name, genotype, chromosome ID, and cM position. (If <code>include.pos.info=TRUE</code>, we take <code>rotate=TRUE</code>.)</p> </td></tr> <tr valign="top"><td><code>rotate</code></td> <td> <p>If TRUE, return matrix with individuals as columns and positions/genotypes as rows. If FALSE, rows correspond to individuals.</p> </td></tr> </table> <h3>Value</h3> <p>A matrix containing genotype probabilities. Multiple chromosomes and the multiple genotypes at each position are pasted together. </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="pull.geno.html">pull.geno</a></code>, <code><a href="pull.argmaxgeno.html">pull.argmaxgeno</a></code>, <code><a href="pull.draws.html">pull.draws</a></code>, <code><a href="calc.genoprob.html">calc.genoprob</a></code> </p> <h3>Examples</h3> <pre> data(listeria) listeria <- calc.genoprob(listeria, step=1, stepwidth="max") pr <- pull.genoprob(listeria, chr=c(5,13), omit.first.prob=TRUE, include.pos.info=TRUE, rotate=TRUE) pr[1:5,1:10] </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>