EVOLUTION-MANAGER
Edit File: summary.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: Summarize the results a genome scan to map a QTL to a...</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 summary.scanPhyloQTL {qtl}"><tr><td>summary.scanPhyloQTL {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Summarize the results a genome scan to map a QTL to a phylogenetic tree</h2> <h3>Description</h3> <p>Print the maximum LOD scores for each partition on each chromosome, from the results of <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanPhyloQTL' summary(object, format=c("postprob", "lod"), threshold, ...) </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>format</code></td> <td> <p>Indicates whether to provide LOD scores or approximate posterior probabilities; see Details below.</p> </td></tr> <tr valign="top"><td><code>threshold</code></td> <td> <p>A threshold determining which chromosomes should be output; see Details below.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Details</h3> <p>This function is used to report chromosomes deemed interesting from a one-QTL genome scan to map QTL to a phylogenetic tree (by <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>). </p> <p>For <code>format="lod"</code>, the output contains the maximum LOD score for each partition on each chromosome (which do not necessarily occur at the same position). The position corresponds to the peak location for the partition with the largest LOD score on that chromosome. The last column is the overall maximum LOD (across partitions) on that chromosome. The second-to-last column is the inferred partition (i.e., that with the largest LOD score. The third-to-last column is the difference between the LOD score for the best partition and that for the second-best. </p> <p>For <code>format="postprob"</code>, the final column contains the maximum LOD score across partitions. But instead of providing the LOD scores for each partition, these are converted to approximate posterior probabilities under the assumption of a single diallelic QTL on that chromosome: on each chromosome, we take <i>10^LOD</i> for the partitions and rescale them to sum to 1. </p> <p>The <code>threshold</code> argument is applied to the last column (the maximum LOD score across partitions). </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="max.scanPhyloQTL.html">max.scanPhyloQTL</a></code>, <code><a href="summary.scanone.html">summary.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>