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<!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: Plot the proportion of missing genotype information</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 plotInfo {qtl}"><tr><td>plotInfo {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot the proportion of missing genotype information</h2> <h3>Description</h3> <p>Plot a measure of the proportion of missing information in the genotype data. </p> <h3>Usage</h3> <pre> plotInfo(x, chr, method=c("entropy","variance","both"), step=1, off.end=0, error.prob=0.001, map.function=c("haldane","kosambi","c-f","morgan"), alternate.chrid=FALSE, fourwaycross=c("all", "AB", "CD"), include.genofreq=FALSE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</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>Optional vector indicating the chromosomes to plot. 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>method</code></td> <td> <p>Indicates whether to plot the entropy version of the information, the variance version, or both.</p> </td></tr> <tr valign="top"><td><code>step</code></td> <td> <p>Maximum distance (in cM) between positions at which the missing information is calculated, though for <code>step=0</code>, it is are calculated only at the marker locations.</p> </td></tr> <tr valign="top"><td><code>off.end</code></td> <td> <p>Distance (in cM) past the terminal markers on each chromosome to which the genotype probability calculations will be carried.</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 or Carter-Falconer map function when converting genetic distances into recombination fractions.</p> </td></tr> <tr valign="top"><td><code>alternate.chrid</code></td> <td> <p>If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.</p> </td></tr> <tr valign="top"><td><code>fourwaycross</code></td> <td> <p>For a phase-known four-way cross, measure missing genotype information overall (<code>"all"</code>), or just for the alleles from the first parent (<code>"AB"</code>) or from the second parent (<code>"CD"</code>).</p> </td></tr> <tr valign="top"><td><code>include.genofreq</code></td> <td> <p>If TRUE, estimated genotype frequencies (from the results of <code><a href="calc.genoprob.html">calc.genoprob</a></code> averaged across the individuals) are included as additional columns in the output.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>The entropy version of the missing information: for a single individual at a single genomic position, we measure the missing information as <i>H = sum p[g] log p[g] / log n</i>, where <i>p[g]</i> is the probability of the genotype <i>g</i>, and <i>n</i> is the number of possible genotypes, defining <i>0 log 0 = 0</i>. This takes values between 0 and 1, assuming the value 1 when the genotypes (given the marker data) are equally likely and 0 when the genotypes are completely determined. We calculate the missing information at a particular position as the average of <i>H</i> across individuals. For an intercross, we don't scale by <i>\log n</i> but by the entropy in the case of genotype probabilities (1/4, 1/2, 1/4). </p> <p>The variance version of the missing information: we calculate the average, across individuals, of the variance of the genotype distribution (conditional on the observed marker data) at a particular locus, and scale by the maximum such variance. </p> <p>Calculations are done in C (for the sake of speed in the presence of little thought about programming efficiency) and the plot is created by a call to <code><a href="plot.scanone.html">plot.scanone</a></code>. </p> <p>Note that <code><a href="summary.scanone.html">summary.scanone</a></code> may be used to display the maximum missing information on each chromosome. </p> <h3>Value</h3> <p>An object with class <code>scanone</code>: a data.frame with columns the chromosome IDs and cM positions followed by the entropy and/or variance version of the missing information. </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="plot.scanone.html">plot.scanone</a></code>, <code><a href="plot.missing.html">plotMissing</a></code>, <code><a href="calc.genoprob.html">calc.genoprob</a></code>, <code><a href="geno.table.html">geno.table</a></code> </p> <h3>Examples</h3> <pre> data(hyper) plotInfo(hyper,chr=c(1,4)) # save the results and view maximum missing info on each chr info <- plotInfo(hyper) summary(info) plotInfo(hyper, bandcol="gray70") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>