ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

Lifecycle: stable R-CMD-check codecov CRAN status License: GPL v3

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:


You can install the released version of ldsep from CRAN with:


And the development version from GitHub with:

# install.packages("devtools")


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

  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

  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 a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.