EVOLUTION-MANAGER
Edit File: droponemarker.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: Drop one marker at a time and determine effect on genetic map</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 droponemarker {qtl}"><tr><td>droponemarker {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Drop one marker at a time and determine effect on genetic map</h2> <h3>Description</h3> <p>Drop one marker at a time from a genetic map and calculate the change in log likelihood and in the chromosome length, in order to identify problematic markers. </p> <h3>Usage</h3> <pre> droponemarker(cross, chr, error.prob=0.0001, map.function=c("haldane","kosambi","c-f","morgan"), m=0, p=0, maxit=4000, tol=1e-6, sex.sp=TRUE, verbose=TRUE) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>cross</code></td> <td> <p>An object of class <code>cross</code>. See <code><a href="read.cross.html">read.cross</a></code> for details.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>A vector specifying which chromosomes to test for the position of the marker. 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>error.prob</code></td> <td> <p>Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).</p> </td></tr> <tr valign="top"><td><code>map.function</code></td> <td> <p>Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions. (Ignored if m > 0.)</p> </td></tr> <tr valign="top"><td><code>m</code></td> <td> <p>Interference parameter for the chi-square model for interference; a non-negative integer, with m=0 corresponding to no interference. This may be used only for a backcross or intercross.</p> </td></tr> <tr valign="top"><td><code>p</code></td> <td> <p>Proportion of chiasmata from the NI mechanism, in the Stahl model; p=0 gives a pure chi-square model. This may be used only for a backcross or intercross.</p> </td></tr> <tr valign="top"><td><code>maxit</code></td> <td> <p>Maximum number of EM iterations to perform.</p> </td></tr> <tr valign="top"><td><code>tol</code></td> <td> <p>Tolerance for determining convergence.</p> </td></tr> <tr valign="top"><td><code>sex.sp</code></td> <td> <p>Indicates whether to estimate sex-specific maps; this is used only for the 4-way cross.</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print information on progress; if > 1, print even more information.</p> </td></tr> </table> <h3>Value</h3> <p>A data frame (actually, an object of class <code>"scanone"</code>, so that one may use <code><a href="plot.scanone.html">plot.scanone</a></code>, <code><a href="summary.scanone.html">summary.scanone</a></code>, etc.) with each row being a marker. The first two columns are the chromosome ID and position. The third column is a LOD score comparing the hypothesis that the marker is not linked to the hypothesis that it belongs at that position. </p> <p>In the case of a 4-way cross, with <code>sex.sp=TRUE</code>, there are two additional columns with the change in the estimated female and male genetic lengths of the respective chromosome, upon deleting that marker. With <code>sex.sp=FALSE</code>, or for other types of crosses, there is one additional column, with the change in estimated genetic length of the respective chromosome, when the marker is omitted. </p> <p>A well behaved marker will have a negative LOD score and a small change in estimated genetic length. A poorly behaved marker will have a large positive LOD score and a large change in estimated genetic length. But note that dropping the first or last marker on a chromosome could result in a large change in estimated length, even if they are not badly behaved; for these markers one should focus on the LOD scores, with a large positive LOD score being bad. </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>tryallpositions</code>, <code><a href="est.map.html">est.map</a></code>, <code><a href="ripple.html">ripple</a></code>, <code><a href="est.rf.html">est.rf</a></code>, <code><a href="switch.order.html">switch.order</a></code>, <code><a href="movemarker.html">movemarker</a></code>, <code><a href="drop.markers.html">drop.markers</a></code> </p> <h3>Examples</h3> <pre> data(fake.bc) droponemarker(fake.bc, 7, error.prob=0, verbose=FALSE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>