EVOLUTION-MANAGER
Edit File: interpPositions.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: Interpolate positions from one map to another</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 interpPositions {qtl}"><tr><td>interpPositions {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Interpolate positions from one map to another</h2> <h3>Description</h3> <p>On the basis of a pair of marker maps with common markers, take positions along one map and interpolate (or, past the terminal markers on a chromosome, extrapolate) their positions on the second map. </p> <h3>Usage</h3> <pre> interpPositions(oldpositions, oldmap, newmap) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>oldpositions</code></td> <td> <p>A data frame with two columns: <code>chr</code> (chromosome identifiers) and <code>pos</code> (positions, along <code>oldmap</code>).</p> </td></tr> <tr valign="top"><td><code>oldmap</code></td> <td> <p>An object of class <code>"map"</code>; see <code><a href="sim.map.html">sim.map</a></code> for details.</p> </td></tr> <tr valign="top"><td><code>newmap</code></td> <td> <p>An object of class <code>"map"</code>, with the same chromosomes and markers as <code>oldmap</code>.</p> </td></tr> </table> <h3>Details</h3> <p>In this explanation, take <code>oldmap</code> and <code>newmap</code> to be the physical and genetic maps, respectively. </p> <p>We use linear interpolation within each interval, assuming a constant recombination rate within the interval. Past the terminal markers, we use linear extrapolation, using the chromosome-wide average recombination rate. </p> <h3>Value</h3> <p>The input data frame, <code>oldpositions</code>, with an additional column <code>newpos</code> with the interpolated positions along <code>newmap</code>.</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="shiftmap.html">shiftmap</a></code>, <code><a href="rescalemap.html">rescalemap</a></code>, <code><a href="pull.map.html">pull.map</a></code> </p> <h3>Examples</h3> <pre> data(hyper) # hyper genetic map gmap <- pull.map(hyper) # a fake physical map, with each chromosome starting at 0. pmap <- shiftmap(rescalemap(gmap, 2)) # positions on pmap to determine location on gmap tofind <- data.frame(chr=c(1, 5, 17, "X"), pos=c(220, 20, 105, 10)) rownames(tofind) <- paste("loc", 1:nrow(tofind), sep="") interpPositions(tofind, pmap, gmap) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>