ldshrink

This will take the output of either <code>mldest()</code> or
<code>sldest()</code>, shrink the Fisher-z transformed
correlation estimates using <code>ash()</code>
(Stephens, 2017; Dey and Stephens, 2018), then return
the corresponding correlation estimates. You can obtain estimates of
r^2 by just squaring these estimates.

Estimate haplotypic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.

David Gerard

ldsep

Linkage Disequilibrium Shrinkage Estimation for Polyploids

ldshrink function

<dl><dt>obj</dt>
<dd>An object of class <code>lddf</code>, usually created using
either <code>mldest()</code> or <code>sldest()</code>.</dd>
<dt>...</dt>
<dd>Additional arguments to pass to <code>ash()</code>.</dd></dl>

Arguments

Author

Obtain shrinkage estimates of correlation from output of
mldest() or sldest(). — ldshrink

<dl>

<dt>obj</dt>
<dd>An object of class <code>lddf</code>, usually created using
either <code>mldest()</code> or <code>sldest()</code>.</dd>


<dt>...</dt>
<dd>Additional arguments to pass to <code>ash()</code>.</dd>

</dl>

ldshrink: Obtain shrinkage estimates of correlation from output of `mldest()` or `sldest()`.

Description

Usage

Value

Arguments

Author

References