get_prob_array

This function will calculate the (log) probabilities for all genotype
combinations at two loci given just the haplotype frequencies. This
is under the assumptions of HWE.

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

get_prob_array function

<dl><dt>K</dt>
<dd>The ploidy of the species.</dd>
<dt>prob</dt>
<dd>Haplotype frequencies in the order of (ab, Ab, aB, AB).</dd>
<dt>log_p</dt>
<dd>A logical. Should we return the log-probabilities (<code>TRUE</code>)
or the probabilities (<code>FALSE</code>). Defaults to <code>TRUE</code>.</dd></dl>

Arguments

Author

Obtain the distribution of genotypes given haplotype frequencies under HWE — get_prob_array

<dl>

<dt>K</dt>
<dd>The ploidy of the species.</dd>


<dt>prob</dt>
<dd>Haplotype frequencies in the order of (ab, Ab, aB, AB).</dd>


<dt>log_p</dt>
<dd>A logical. Should we return the log-probabilities (<code>TRUE</code>)
or the probabilities (<code>FALSE</code>). Defaults to <code>TRUE</code>.</dd>

</dl>

get_prob_array: Obtain the distribution of genotypes given haplotype frequencies under HWE

Description

Usage

Value

Arguments

Author

Examples