EVOLUTION-MANAGER
Edit File: formMarkerCovar.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: Create matrix of marker covariates for QTL analysis</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 formMarkerCovar {qtl}"><tr><td>formMarkerCovar {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Create matrix of marker covariates for QTL analysis</h2> <h3>Description</h3> <p>Pull out a matrix of genotypes or genotype probabilities to use markers as covariates in QTL analysis. </p> <h3>Usage</h3> <pre>formMarkerCovar(cross, markers, method=c("prob", "imp", "argmax"), ...)</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>markers</code></td> <td> <p>A vector of character strings of marker or pseudomarker names. Pseudomarker names may be of the form <code>"5@21.5"</code> (for chr 5 at 21.5 cM), but then all names must be of this form.</p> </td></tr> <tr valign="top"><td><code>method</code></td> <td> <p>If <code>method="prob"</code>, the genotype probabilities from <code><a href="calc.genoprob.html">calc.genoprob</a></code> are used; otherwise we use <code><a href="fill.geno.html">fill.geno</a></code> to impute missing data, with this method.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code><a href="fill.geno.html">fill.geno</a></code>, if necessary.</p> </td></tr> </table> <h3>Value</h3> <p>A matrix containing genotype probabilities or genotype indicators, suitable for use as covariates in <code><a href="scanone.html">scanone</a></code>. </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.genoprob.html">pull.genoprob</a></code>, <code><a href="fill.geno.html">fill.geno</a></code>, <code><a href="scanone.html">scanone</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper, step=0) peakMarker <- "D4Mit164" X <- formMarkerCovar(hyper, peakMarker) out <- scanone(hyper, addcovar=X) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>