EVOLUTION-MANAGER
Edit File: makeqtl.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: Make a qtl object</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 makeqtl {qtl}"><tr><td>makeqtl {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Make a qtl object</h2> <h3>Description</h3> <p>This function takes a cross object and specified chromosome numbers and positions and pulls out the genotype probabilities or imputed genotypes at the nearest pseudomarkers, for later use by the function <code><a href="fitqtl.html">fitqtl</a></code>. </p> <h3>Usage</h3> <pre> makeqtl(cross, chr, pos, qtl.name, what=c("draws","prob")) </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>Vector indicating the chromosome for each QTL. (These should be character strings referring to the chromosomes by name.)</p> </td></tr> <tr valign="top"><td><code>pos</code></td> <td> <p>Vector (of same length as <code>chr</code>) indicating the positions on the chromosome to be taken. If there is no marker or pseudomarker at a position, the nearest position is used.</p> </td></tr> <tr valign="top"><td><code>qtl.name</code></td> <td> <p>Optional user-specified name for each QTL, used in the drop-one-term ANOVA table in <code><a href="fitqtl.html">fitqtl</a></code>. If unspecified, the names will be of the form <code>"Chr1@10"</code> for a QTL on Chromsome 1 at 10 cM.</p> </td></tr> <tr valign="top"><td><code>what</code></td> <td> <p>Indicates whether to pull out the imputed genotypes or the genotype probabilities.</p> </td></tr> </table> <h3>Details</h3> <p>This function will take out the genotype probabilities and imputed genotypes if they are present in the input <code>cross</code> object. If both fields are missing in the input object, the function will report an error. Before running this function, the user must have first run either <code><a href="sim.geno.html">sim.geno</a></code> (for <code>what="draws"</code>) or <code><a href="calc.genoprob.html">calc.genoprob</a></code> (for <code>what="prob"</code>). </p> <h3>Value</h3> <p>An object of class <code>qtl</code> with the following elements (though only one of <code>geno</code> and <code>prob</code> will be included, according to whether <code>what</code> is given as <code>"draws"</code> or <code>"prob"</code>): </p> <table summary="R valueblock"> <tr valign="top"><td><code><code>geno</code></code></td> <td> <p>Imputed genotypes.</p> </td></tr> <tr valign="top"><td><code><code>prob</code></code></td> <td> <p>Genotype probabilities.</p> </td></tr> <tr valign="top"><td><code><code>name</code></code></td> <td> <p>User-defined name for each QTL, or a name of the form <code>"Chr1@10"</code>.</p> </td></tr> <tr valign="top"><td><code><code>altname</code></code></td> <td> <p>QTL names of the form <code>"Q1"</code>, <code>"Q2"</code>, etc.</p> </td></tr> <tr valign="top"><td><code><code>chr</code></code></td> <td> <p>Input vector of chromosome numbers.</p> </td></tr> <tr valign="top"><td><code><code>pos</code></code></td> <td> <p>Input vector of chromosome positions.</p> </td></tr> <tr valign="top"><td><code><code>n.qtl</code></code></td> <td> <p>Number of QTLs.</p> </td></tr> <tr valign="top"><td><code><code>n.ind</code></code></td> <td> <p>Number of individuals.</p> </td></tr> <tr valign="top"><td><code><code>n.gen</code></code></td> <td> <p>A vector indicating the number of genotypes for each QTL.</p> </td></tr> </table> <h3>Author(s)</h3> <p>Hao Wu; Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a></p> <h3>See Also</h3> <p><code><a href="fitqtl.html">fitqtl</a></code>, <code><a href="calc.genoprob.html">calc.genoprob</a></code>, <code><a href="sim.geno.html">sim.geno</a></code>, <code><a href="dropfromqtl.html">dropfromqtl</a></code>, <code><a href="replaceqtl.html">replaceqtl</a></code>, <code><a href="addtoqtl.html">addtoqtl</a></code>, <code><a href="summary.qtl.html">summary.qtl</a></code>, <code><a href="reorderqtl.html">reorderqtl</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) # take out several QTLs and make QTL object qc <- c("1", "6", "13") qp <- c(25.8, 33.6, 18.63) fake.f2 <- subset(fake.f2, chr=qc) fake.f2 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001) qtl <- makeqtl(fake.f2, qc, qp, what="draws") summary(qtl) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>