Estimate haplotypic or composite pairwise linkage disequilibrium (LD)in polyploids, using either genotypes or genotype likelihoods. Supportis provided to estimate the popular measures of LD: the LD coefficient\(D\), the standardized LD coefficient\(D'\), and the Pearson correlationcoefficient\(r\). All estimates arereturned with corresponding standard errors. These estimates andstandard errors can then be used for shrinkage estimation. The methodsare described in Gerard (2021a) and Gerard (2021b).
The main functions are:
ldfast(): Fast, moment-based approach to estimatepairwise LD in the presence of genotype uncertainty.ldest(): Estimates pairwise LD via maximumlikelihood.mldest(): Iteratively applyldest()acrossmany pairs of SNPs.sldest(): Iteratively applyldest()alonga sliding window of fixed length.plot.lddf(): Plot method for the output ofmldest()andsldest().format_lddf(): Format the output ofmldest()andsldest()into a matrix.ldshrink(): Shrink correlation estimates using adaptiveshrinkage (Stephens, 2017; Dey and Stephens, 2018).
Installation
You can install the released version of ldsep fromCRAN with:
install.packages("ldsep")And the development version fromGitHub with:
# install.packages("devtools")devtools::install_github("dcgerard/ldsep")Citation
To citeldsep in publications use:
Gerard, David (2021). “Pairwise Linkage Disequilibrium Estimation forPolyploids.”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 useldfast(), please cite:
Gerard, David (2021). “Scalable Bias-corrected Linkage DisequilibriumEstimation 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},}Code of Conduct
Please note that the ldsep project is released with aContributorCode of Conduct. By contributing to this project, you agree to abideby its terms.
References
Dey, Kushal K., and Matthew Stephens (2018). “CorShrink:Empirical Bayes shrinkage estimation of correlations, withapplications.”bioRxiv.doi:10.1101/368316
Gerard, David (2021a). “Pairwise Linkage DisequilibriumEstimation for Polyploids.”Molecular Ecology Resources,21(4), 1230–1242.doi:10.1111/1755-0998.13349.
Gerard, David (2021b). “Scalable Bias-corrected LinkageDisequilibrium 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
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