plotMissing

Plot a grid showing which genotypes are missing.

hplot

Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.

Karl Broman

Tools for Analyzing QTL Experiments

Hao Wu

Gary Churchill

Saunak Sen

Danny Arends

Robert Corty

Timothee Flutre

Ritsert Jansen

Pjotr Prins

Lars Ronnegard

Rohan Shah

Laura Shannon

Quoc Tran

Aaron Wolen

Brian Yandell

R Core Team 

plotMissing function

<dl> <dt>x</dt>
<dd>An object of class <code>cross</code>. See
 <code>read.cross</code> for details.</dd> <dt>chr</dt>
<dd>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.</dd> <dt>reorder</dt>
<dd>Specify whether to reorder individuals according to
 their phenotypes.<table class="table">
<tr><td>FALSE</td><td>Don't reorder</td></tr>
<tr><td>TRUE</td><td>Reorder according to the sum of the phenotypes</td></tr>
<tr><td>n</td><td>Reorder according to phenotype n</td></tr>
</table>
</dd> <dt>main</dt>
<dd>Title to place on plot.</dd> <dt>alternate.chrid</dt>
<dd>If TRUE and more than one chromosome is
 plotted, alternate the placement of chromosome
 axis labels, so that they may be more easily distinguished.</dd> <dt>...</dt>
<dd>Ignored at this point.</dd></dl>

Arguments

Karl W Broman, <a href="/link/broman%40wisc.edu?package=qtl&version=1.70" data-mini-rdoc="qtl::broman@wisc.edu">broman@wisc.edu</a>

Author

Plot grid of missing genotypes — plotMissing

<dl>

 <dt>x</dt>
<dd>An object of class <code>cross</code>. See
 <code>read.cross</code> for details.</dd>

 <dt>chr</dt>
<dd>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.</dd>

 <dt>reorder</dt>
<dd>Specify whether to reorder individuals according to
 their phenotypes.<table class='table'>
<tr><td>FALSE</td><td>Don't reorder</td></tr>
<tr><td>TRUE</td><td>Reorder according to the sum of the phenotypes</td></tr>
<tr><td>n</td><td>Reorder according to phenotype n</td></tr>
</table>
</dd>

 <dt>main</dt>
<dd>Title to place on plot.</dd>

 <dt>alternate.chrid</dt>
<dd>If TRUE and more than one chromosome is
 plotted, alternate the placement of chromosome
 axis labels, so that they may be more easily distinguished.</dd>

 <dt>...</dt>
<dd>Ignored at this point.</dd>

</dl>

Karl W Broman, <a href='mailto:broman@wisc.edu'>broman@wisc.edu</a>

Plot grid of missing genotypes

plotMissing: Plot grid of missing genotypes

Description

Usage

Value

Arguments

Author

Details

See Also

Examples

FALSE	Don't reorder
TRUE	Reorder according to the sum of the phenotypes
n	Reorder according to phenotype n