EVOLUTION-MANAGER
Edit File: pickMarkerSubset.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 the largest subset of markers that are some distance...</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 pickMarkerSubset {qtl}"><tr><td>pickMarkerSubset {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Identify the largest subset of markers that are some distance apart</h2> <h3>Description</h3> <p>Identify the largest subset of markers for which no two adjacent markers are separated by less than some specified distance; if weights are provided, find the marker subset for which the sum of the weights is maximized. </p> <h3>Usage</h3> <pre> pickMarkerSubset(locations, min.distance, weights) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>locations</code></td> <td> <p>A vector of marker locations.</p> </td></tr> <tr valign="top"><td><code>min.distance</code></td> <td> <p>Minimum distance between adjacent markers in the chosen subset.</p> </td></tr> <tr valign="top"><td><code>weights</code></td> <td> <p>(Optional) vector of weights for the markers. If missing, we take <code>weights == 1</code>.</p> </td></tr> </table> <h3>Details</h3> <p>Let <i>d[i]</i> be the location of marker <i>i</i>, for <i>i in 1, …, M</i>. We use the dynamic programming algorithm of Broman and Weber (1999) to identify the subset of markers <i>i[1], …, i[k]</i> for which <i>d(i[j+1]) - d(i[j]) <=</i> <code>min.distance</code> and <i>sum w(i[j])</i> is maximized. </p> <p>If there are multiple optimal subsets, we pick one at random. </p> <h3>Value</h3> <p>A vector of marker names.</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. and Weber, J. L. (1999) Method for constructing confidently ordered linkage maps. <em>Genet. Epidemiol.</em>, <b>16</b>, 337–343. </p> <h3>See Also</h3> <p><code><a href="drop.markers.html">drop.markers</a></code>, <code><a href="pull.markers.html">pull.markers</a></code>, <code><a href="findDupMarkers.html">findDupMarkers</a></code> </p> <h3>Examples</h3> <pre> data(hyper) # subset of markers on chr 4 spaced >= 5 cM pickMarkerSubset(pull.map(hyper)[[4]], 5) # no. missing genotypes at each chr 4 marker n.missing <- nmissing(subset(hyper, chr=4), what="mar") # weight by -log(prop'n missing), but don't let 0 missing go to +Inf wts <- -log( (n.missing+1) / (nind(hyper)+1) ) # subset of markers on chr 4 spaced >= 5 cM, with weights = -log(prop'n missing) pickMarkerSubset(pull.map(hyper)[[4]], 5, wts) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>