slcor

Calculates the pairwise Pearson correlation between all columns
within a fixed window size (<code>win</code>)
using the <code>use = "pairwise.complete.obs"</code> option
from <code><a href="/link/cor?package=ldsep&version=2.1.5" data-mini-rdoc="ldsep::cor">cor</a>()</code>. That is, the correlation
between each pair of variables is computed using all complete pairs
of observations on those variables.

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

slcor function

<dl><dt>x</dt>
<dd>A numeric matrix. The variables index the columns.</dd>
<dt>win</dt>
<dd>The size of the window. Defaults to 1.</dd></dl>

Arguments

Author

Calculates the pairwise Pearson correlation between all columns
within a fixed window size (<code>win</code>)
using the <code>use = "pairwise.complete.obs"</code> option
from <code><a href='https://rdrr.io/r/stats/cor.html'>cor</a>()</code>. That is, the correlation
between each pair of variables is computed using all complete pairs
of observations on those variables.

Sliding window correlation — slcor

<dl>

<dt>x</dt>
<dd>A numeric matrix. The variables index the columns.</dd>


<dt>win</dt>
<dd>The size of the window. Defaults to 1.</dd>

</dl>

slcor: Sliding window correlation

Description

Usage

Value

Arguments

Author

Examples