EVOLUTION-MANAGER
Edit File: replaceqtl.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: Replace a QTL in a qtl object with a different position</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 replaceqtl {qtl}"><tr><td>replaceqtl {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Replace a QTL in a qtl object with a different position</h2> <h3>Description</h3> <p>This function replaces a QTL or QTLs in a qtl object with a different position. </p> <h3>Usage</h3> <pre> replaceqtl(cross, qtl, index, chr, pos, qtl.name, drop.lod.profile=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>qtl</code></td> <td> <p>A qtl object, as created by <code><a href="makeqtl.html">makeqtl</a></code>.</p> </td></tr> <tr valign="top"><td><code>index</code></td> <td> <p>Numeric index indicating the QTL to be replaced.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Vector (of same length as <code>index</code>) indicating the chromosomes for the new QTL.</p> </td></tr> <tr valign="top"><td><code>pos</code></td> <td> <p>Vector (of same length as <code>index</code>) indicating the positions for the new QTL. If there is no marker or pseudomarker at a position, the nearest position is used.</p> </td></tr> <tr valign="top"><td><code>qtl.name</code></td> <td> <p>Optional vector (of same length as <code>index</code>) of user-specified names for each new QTL, used in the drop-one-term ANOVA table in <code><a href="fitqtl.html">fitqtl</a></code>. If unspecified, the names will be of the form <code>"Chr1@10"</code> for a QTL on Chromsome 1 at 10 cM.</p> </td></tr> <tr valign="top"><td><code>drop.lod.profile</code></td> <td> <p>If TRUE, remove any LOD profiles from the object.</p> </td></tr> </table> <h3>Value</h3> <p>The input <code>qtl</code> object, but with some QTL replaced by new ones. See <code><a href="makeqtl.html">makeqtl</a></code> for details on the format. </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="makeqtl.html">makeqtl</a></code>, <code><a href="fitqtl.html">fitqtl</a></code>, <code><a href="dropfromqtl.html">dropfromqtl</a></code>, <code><a href="addtoqtl.html">addtoqtl</a></code>, <code><a href="reorderqtl.html">reorderqtl</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) # take out several QTLs and make QTL object qc <- c(1, 6, 13) qp <- c(25.8, 33.6, 18.63) fake.f2 <- subset(fake.f2, chr=qc) fake.f2 <- calc.genoprob(fake.f2, step=2, err=0.001) qtl <- makeqtl(fake.f2, qc, qp, what="prob") qtl <- replaceqtl(fake.f2, qtl, 2, 6, 48.1) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>