EVOLUTION-MANAGER
Edit File: inferredpartitions.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: Identify inferred partitions in mapping 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 inferredpartitions {qtl}"><tr><td>inferredpartitions {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Identify inferred partitions in mapping QTL to a phylogenetic tree</h2> <h3>Description</h3> <p>Identify the inferred partitions for a chromosome from the results of scanPhyloQTL. </p> <h3>Usage</h3> <pre> inferredpartitions(output, chr, lodthreshold, probthreshold=0.9) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>output</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>A character string indicating the chromosome to consider. (It can also be a number, but it's then converted to a character string.)</p> </td></tr> <tr valign="top"><td><code>lodthreshold</code></td> <td> <p>LOD threshold; if maximum LOD score is less than this, the null model is considered.</p> </td></tr> <tr valign="top"><td><code>probthreshold</code></td> <td> <p>Threshold on posterior probabilities. See Details below.</p> </td></tr> </table> <h3>Details</h3> <p>We consider a single chromosome, and take the maximum LOD score for each partition on that chromosome. The presence of a QTL is inferred if at least one partition has LOD score greater than <code>lodthreshold</code>. In this case, we then convert the LOD scores for the partitions to approximate posterior probabilities by taking <i>10^LOD</i> and then rescaling them to sum to 1. These are sorted from largest to smallest, and we then take as the inferred partitions the smallest set whose posterior probabilities cumulatively add up to at least <code>probthreshold</code>. </p> <h3>Value</h3> <p>A vector of character strings. If the null model (no QTL) is inferred, the output is <code>"null"</code>. Otherwise, it is the set of inferred partitions. </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.scanPhyloQTL.html">max.scanPhyloQTL</a></code>, <code><a href="simPhyloQTL.html">simPhyloQTL</a></code> </p> <h3>Examples</h3> <pre> # 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 ## Not run: x <- lapply(x, calc.genoprob, step=2) # scan genome, at each position trying all possible partitions out <- scanPhyloQTL(x, method="hk") # inferred partitions inferredpartitions(out, chr=3, lodthreshold=3) # inferred partitions with prob'y threshold = 0.95 inferredpartitions(out, chr=3, lodthreshold=3, probthreshold=0.95) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>