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

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=1.66" 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>

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