zshrink

This function is a wrapper for adaptive shrinkage (Stephens, 2017) on the
Fisher-z transformed estimates of the Pearson correlation. This approach
was proposed in Dey and Stephens (2018) but is re-implemented here for now
since the CorShrink package is not available on CRAN.

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

zshrink function

<dl><dt>zmat</dt>
<dd>The matrix of Fisher-z transformed correlation estimates.</dd>
<dt>smat</dt>
<dd>The matrix of standard errors of the Fisher-z transformed
correlation estimates.</dd>
<dt>...</dt>
<dd>Additional arguments to pass to <code>ash()</code>.</dd></dl>

Arguments

Author

Shrinks Fisher-z transformed correlation estimates and returns resulting
correlation estimates. — zshrink

<dl>

<dt>zmat</dt>
<dd>The matrix of Fisher-z transformed correlation estimates.</dd>


<dt>smat</dt>
<dd>The matrix of standard errors of the Fisher-z transformed
correlation estimates.</dd>


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

</dl>

zshrink: Shrinks Fisher-z transformed correlation estimates and returns resulting correlation estimates.

Description

Usage

Value

Arguments

Author

References