pvcalc

Given a matrix of prior probabilities for the genotypes at each SNP,
this function will calculate the prior variance of genotypes.

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

pvcalc function

<dl><dt>priormat</dt>
<dd>A matrix of prior genotype probabilities. Element
<code>priormat[i, j]</code> is the prior probability of dosage <code>j</code>
at SNP <code>i</code>.</dd></dl>

Arguments

Author

Calculate prior variances from a matrix of prior genotype probabilities. — pvcalc

<dl>

<dt>priormat</dt>
<dd>A matrix of prior genotype probabilities. Element
<code>priormat[i, j]</code> is the prior probability of dosage <code>j</code>
at SNP <code>i</code>.</dd>

</dl>

pvcalc: Calculate prior variances from a matrix of prior genotype probabilities.

Description

Usage

Value

Arguments

Author

Examples