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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, David (2021). “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Molecular Ecology Resources, 21(4), 1230–1242. 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 = {21},
number = {4},
pages = {1230--1242},
}If you use ldfast(), please cite:
Gerard, David (2021). “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.” Heredity, 127(4), 357–362. doi:10.1038/s41437-021-00462-5.
A BibTeX entry for LaTeX users is
@Article{,
title = {Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty},
author = {David Gerard},
journal = {Heredity},
year = {2021},
volume = {127},
number = {4},
pages = {357--362},
doi = {10.1038/s41437-021-00462-5},
}Please note that the ldsep project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Dey, Kushal K., and Matthew Stephens (2018). “CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications.” bioRxiv. doi:10.1101/368316
Gerard, David (2021a). “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Molecular Ecology Resources, 21(4), 1230–1242. doi:10.1111/1755-0998.13349.
Gerard, David (2021b). “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.” Heredity, 127(4), 357–362. doi:10.1038/s41437-021-00462-5.
Stephens, Matthew (2017). “False discovery rates: a new deal.” Biostatistics 18(2), 275–294. doi:10.1093/biostatistics/kxw041
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.