EVOLUTION-MANAGER
Edit File: max.scanPhyloQTL.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: Maximum peak in genome scan to map a QTL to a phylogenetic...</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 max.scanPhyloQTL {qtl}"><tr><td>max.scanPhyloQTL {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Maximum peak in genome scan to map a QTL to a phylogenetic tree</h2> <h3>Description</h3> <p>Print the chromosome with the maximum LOD score across partitions, from the results of <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanPhyloQTL' max(object, chr, format=c("postprob", "lod"), ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>object</code></td> <td> <p>An object output by the function <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>.</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>format</code></td> <td> <p>Indicates whether to provide LOD scores or approximate posterior probabilities; see the help file for <code><a href="summary.scanPhyloQTL.html">summary.scanPhyloQTL</a></code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Details</h3> <p>The output, and the use of the argument <code>format</code>, is as in <code><a href="summary.scanPhyloQTL.html">summary.scanPhyloQTL</a></code>. </p> <h3>Value</h3> <p>An object of class <code>summary.scanPhyloQTL</code>, to be printed by <code>print.summary.scanPhyloQTL</code>. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a></p> <h3>References</h3> <p>Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation. </p> <h3>See Also</h3> <p><code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>, <code><a href="plot.scanPhyloQTL.html">plot.scanPhyloQTL</a></code>, <code><a href="summary.scanPhyloQTL.html">summary.scanPhyloQTL</a></code>, <code><a href="max.scanone.html">max.scanone</a></code>, <code><a href="inferredpartitions.html">inferredpartitions</a></code>, <code><a href="simPhyloQTL.html">simPhyloQTL</a></code> </p> <h3>Examples</h3> <pre> ## Not run: # example map; drop X chromosome data(map10) map10 <- map10[1:19] # simulate data x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"), map=map10, n.ind=150, model=c(1, 50, 0.5, 0)) # run calc.genoprob on each cross x <- lapply(x, calc.genoprob, step=2) # scan genome, at each position trying all possible partitions out <- scanPhyloQTL(x, method="hk") # maximum peak max(out, format="lod") # approximate posterior probabilities at peak max(out, format="postprob") # all peaks above a threshold for LOD(best) - LOD(2nd best) summary(out, threshold=1, format="lod") # all peaks above a threshold for LOD(best), showing approx post'r prob summary(out, format="postprob", threshold=3) # plot of results plot(out) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>