EVOLUTION-MANAGER
Edit File: readMWril.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: Read data for 4- or 8-way RIL</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 readMWril {qtl}"><tr><td>readMWril {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Read data for 4- or 8-way RIL</h2> <h3>Description</h3> <p>Data for a set of 4- or 8-way recombinant inbred lines (RIL) is read from a pair of comma-delimited files and converted into an object of class <code>cross</code>. We require chromosome assignments for the genetic markers, and assume that markers are in their correct order. </p> <h3>Usage</h3> <pre> readMWril(dir="", rilfile, founderfile, type=c("ri4self", "ri4sib", "ri8self", "ri8selfIRIP1", "ri8sib", "bgmagic16"), na.strings=c("-","NA"), rotate=FALSE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>dir</code></td> <td> <p>Directory in which the data files will be found. In Windows, use forward slashes (<code>"/"</code>) or double backslashes (<code>"\\"</code>) to specify directory trees.</p> </td></tr> <tr valign="top"><td><code>rilfile</code></td> <td> <p>Comma-delimited file for the RIL, in the <code>"csv"</code> format described in the help file for <code><a href="read.cross.html">read.cross</a></code>.</p> </td></tr> <tr valign="top"><td><code>founderfile</code></td> <td> <p>File with founder strains' genotypes, in the same orientation as the <code>rilfile</code>, but with just marker names and the founders' marker genotypes.</p> </td></tr> <tr valign="top"><td><code>type</code></td> <td> <p>The type of RIL.</p> </td></tr> <tr valign="top"><td><code>na.strings</code></td> <td> <p>A vector of strings which are to be interpreted as missing values. For the <code>csv</code> formats, these are interpreted globally for the entire file, so missing value codes in phenotypes must not be valid genotypes, and vice versa. For the <code>gary</code> format, these are used only for the phenotype data.</p> </td></tr> <tr valign="top"><td><code>rotate</code></td> <td> <p>If TRUE, the <code>rilfile</code> and <code>founderfile</code> are rotated (really transposed), with rows corresponding to markers and columns corresponding to individuals.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Additional arguments, passed to the function <code><a href="../../utils/html/read.table.html">read.table</a></code> in the case of <code>csv</code> and <code>csvr</code> formats. In particular, one may use the argument <code>sep</code> to specify the field separator (the default is a comma) and <code>dec</code> to specify the character used for the decimal point (the default is a period).</p> </td></tr> </table> <h3>Details</h3> <p>The <code>rilfile</code> should include a phenotype <code>cross</code> containing character strings of the form <code>ABCDEFGH</code>, indicating the cross used to generate each RIL. The genotypes should be coded as <b>integers</b> (e.g., 1 and 2). </p> <p>The founder strains in the <code>founderfile</code> should be the strains <code>A</code>, <code>B</code>, <code>C</code>, ..., as indicated in the <code>cross</code> phenotype. </p> <p>The default arrangement of the files is to have markers as columns and individuals/founders as rows. If <code>rotate=TRUE</code>, do the opposite: markers as rows and individuals/founders as columns. </p> <h3>Value</h3> <p>An object of class <code>cross</code>; see the help file for <code><a href="read.cross.html">read.cross</a></code> for details. </p> <p>An additional component <code>crosses</code> is included; this is a matrix indicating the crosses used to generate the RIL. </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="read.cross.html">read.cross</a></code>, <code><a href="sim.cross.html">sim.cross</a></code> </p> <h3>Examples</h3> <pre> ## Not run: ril <- read.cross("../Data", "ril_data.csv", "founder_geno.csv", "ri4self", rotate=TRUE) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>