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Edit File: inferFounderHap.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: Crude reconstruction of founder haplotypes in multi-parent...</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 inferFounderHap {qtl}"><tr><td>inferFounderHap {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Crude reconstruction of founder haplotypes in multi-parent RIL</h2> <h3>Description</h3> <p>Uses groups of adjacent markers to infer the founder haplotypes in SNP data on multi-parent recombinant inbred lines. </p> <h3>Usage</h3> <pre> inferFounderHap(cross, chr, max.n.markers=15) </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>Indicator of chromosome to consider. If multiple chromosomes are selected, only the first is used.</p> </td></tr> <tr valign="top"><td><code>max.n.markers</code></td> <td> <p>Maximum number of adjacent markers to consider.</p> </td></tr> </table> <h3>Details</h3> <p>We omit SNPs for which any of the founders are missing. </p> <p>We then consider groups of adjacent SNPs, looking for founder haplotypes that are unique; RIL sharing such a unique haplotype are then inferred to have that founder's DNA. </p> <p>We consider each marker as the center of a haplotype, and consider haplotypes of size 1, 3, 5, ..., <code>max.n.markers</code>. We end the extension of the haplotypes when all founders have a unique haplotype. </p> <h3>Value</h3> <p>A matrix of dimension <code>nind(cross)</code> <i>x</i> no. markers, with the inferred founder origin for each line at each marker. </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="sim.geno.html">sim.geno</a></code>, <code><a href="calc.genoprob.html">calc.genoprob</a></code>, <code><a href="fill.geno.html">fill.geno</a></code>, <code><a href="argmax.geno.html">argmax.geno</a></code> </p> <h3>Examples</h3> <pre> map <- sim.map(100, n.mar=101, include.x=FALSE, eq.spacing=TRUE) founderGeno <- simFounderSnps(map, "8") ril <- sim.cross(map, n.ind=10, type="ri8sib", founderGeno=founderGeno) h <- inferFounderHap(ril, max.n.markers=11) mean(!is.na(h)) # proportion inferred plot(map[[1]], h[1,], ylim=c(0.5, 8.5), xlab="Position", ylab="Genotype") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>