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Edit File: scanPhyloQTL.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: Single-QTL genome scan to map QTL to a phylogenetic tree</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 scanPhyloQTL {qtl}"><tr><td>scanPhyloQTL {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Single-QTL genome scan to map QTL to a phylogenetic tree</h2> <h3>Description</h3> <p>Jointly consider multiple intercrosses with a single diallelic QTL model, considering all possible partitions of the strains into the two QTL allele groups. </p> <h3>Usage</h3> <pre> scanPhyloQTL(crosses, partitions, chr, pheno.col=1, model=c("normal", "binary"), method=c("em", "imp", "hk"), addcovar, maxit=4000, tol=0.0001, useAllCrosses=TRUE, verbose=FALSE) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>crosses</code></td> <td> <p>A list with each component being an intercross, as an object of class <code>cross</code> (see <code><a href="read.cross.html">read.cross</a></code> for details). The names (of the form "AB") indicate the strains in the cross.</p> </td></tr> <tr valign="top"><td><code>partitions</code></td> <td> <p>A vector of character strings of the form "AB|CD" or "A|BCD" indicating the set of paritions of the strains into two allele groups. If missing, all partitions should be considered.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector indicating the chromosomes for which LOD scores should be calculated. 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>pheno.col</code></td> <td> <p>Column number in the phenotype matrix which should be used as the phenotype. This can be a vector of integers; for methods <code>"hk"</code> and <code>"imp"</code> this can be considerably faster than doing them one at a time. One may also give a character strings matching the phenotype names. Finally, one may give a numeric vector of phenotypes, in which case it must have the length equal to the number of individuals in the cross, and there must be either non-integers or values < 1 or > no. phenotypes; this last case may be useful for studying transformations.</p> </td></tr> <tr valign="top"><td><code>model</code></td> <td> <p>The phenotype model: the usual normal model or a model for binary traits</p> </td></tr> <tr valign="top"><td><code>method</code></td> <td> <p>Indicates whether to use the EM algorithm, imputation, or Haley-Knott regression.</p> </td></tr> <tr valign="top"><td><code>addcovar</code></td> <td> <p>Optional set of additive covariates to include in the analysis, as a list with the same length as <code>crosses</code>. They must be numeric vectors or matrices, as for <code><a href="scanone.html">scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>maxit</code></td> <td> <p>Maximum number of iterations for method <code>"em"</code>.</p> </td></tr> <tr valign="top"><td><code>tol</code></td> <td> <p>Tolerance value for determining convergence for method <code>"em"</code>.</p> </td></tr> <tr valign="top"><td><code>useAllCrosses</code></td> <td> <p>If TRUE, use all crosses in the analysis of all partitions, with crosses not segregating the QTL included in the estimation of the residual variance.</p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p>If TRUE, print information about progress.</p> </td></tr> </table> <h3>Details</h3> <p>The aim is to jointly consider multiple intercrosses to not just map QTL but to also, under the assumption of a single diallelic QTL, identify the set of strains with each QTL allele. </p> <p>For each partition (of the strains into two groups) that is under consideration, we pull out the set of crosses that are segregating the QTL, re-code the alleles, and combine the crosses into one large cross. Crosses not segregating the QTL are also used, though with no QTL effects. </p> <p>Additive covariate indicators for the crosses are included in the analysis, to allow for the possibility that there are overall shifts in the phenotypes between crosses. </p> <h3>Value</h3> <p>A data frame, as for the output of <code><a href="scanone.html">scanone</a></code>, though with LOD score columns for each partition that is considered. The result is given class <code>"scanPhyloQTL"</code>. </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a></p> <h3>References</h3> <p>Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation. </p> <h3>See Also</h3> <p><code><a href="plot.scanPhyloQTL.html">plot.scanPhyloQTL</a></code>, <code><a href="summary.scanPhyloQTL.html">summary.scanPhyloQTL</a></code>, <code><a href="max.scanPhyloQTL.html">max.scanPhyloQTL</a></code>, <code><a href="inferredpartitions.html">inferredpartitions</a></code>, <code><a href="simPhyloQTL.html">simPhyloQTL</a></code> </p> <h3>Examples</h3> <pre> # example map; drop X chromosome data(map10) map10 <- map10[1:19] # simulate data x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"), map=map10, n.ind=150, model=c(1, 50, 0.5, 0)) # run calc.genoprob on each cross ## Not run: x <- lapply(x, calc.genoprob, step=2) # scan genome, at each position trying all possible partitions out <- scanPhyloQTL(x, method="hk") # maximum peak max(out, format="lod") # approximate posterior probabilities at peak max(out, format="postprob") # all peaks above a threshold for LOD(best) - LOD(2nd best) summary(out, threshold=1, format="lod") # all peaks above a threshold for LOD(best), showing approx post'r prob summary(out, format="postprob", threshold=3) # plot results plot(out) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>