I posted a package to CRAN to 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 methods are described in Gerard (2021a) and Gerard (2021b).
The main functions are:
ldfast(): Fast, moment-based approach to estimate pairwise LD in
the presence of genotype uncertainty.
ldest(): Estimates pairwise LD via maximum likelihood.
mldest(): Iteratively apply ldest() across many pairs of SNPs.
sldest(): Iteratively apply ldest() along a sliding window of
fixed length.
plot.lddf(): Plot method for the output of mldest() and
sldest().
format_lddf(): Format the output of mldest() and sldest() into
a matrix.
ldshrink(): Shrink correlation estimates using adaptive shrinkage
(Stephens, 2017; Dey and Stephens, 2018).
You can install the released version of ldsep from CRAN with:
install.packages("ldsep")
And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("dcgerard/ldsep")
To cite ldsep in publications use:
Gerard D (2021). “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Molecular Ecology Resources, Accepted Author Manuscript. doi:10.1111/1755-0998.13349.
A BibTeX entry for LaTeX users is
@Article{,
title = {Pairwise Linkage Disequilibrium Estimation for Polyploids},
author = {David Gerard},
journal = {Molecular Ecology Resources},
year = {2021},
doi = {10.1111/1755-0998.13349},
volume = {Accepted Author Manuscript},
}
If you use ldfast(), please cite:
Gerard D (2021). “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.” bioRxiv. doi:10.1101/2021.02.08.430270.
A BibTeX entry for LaTeX users is
@Article{,
title = {Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty},
author = {David Gerard},
journal = {bioRxiv},
year = {2021},
doi = {10.1101/2021.02.08.430270},
}
Dey, Kushal K., and Matthew Stephens. “CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications.” bioRxiv (2018): 368316. doi:10.1101/368316
Gerard, David. “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Molecular Ecology Resources. Accepted Author Manuscript. (2021a) doi:10.1111/1755-0998.13349
Gerard, David. “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.” bioRxiv. (2021b) doi:10.1101/2021.02.08.430270
Stephens, Matthew. “False discovery rates: a new deal.” Biostatistics 18, no. 2 (2017): 275-294. doi:10.1093/biostatistics/kxw041