Estimate gametic 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 (2020).
The main functions are:
ldest(): Estimates pairwise LD.
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
format_lddf(): Format the output of
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:
And the development version from GitHub with:
# install.packages("devtools") devtools::install_github("dcgerard/ldsep")
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.
- Dey, Kushal K., and Matthew Stephens. “CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications.” bioRxiv (2018): 368316.
- Gerard, David. “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Unpublished manuscript (2020).
- Stephens, Matthew. “False discovery rates: a new deal.” Biostatistics 18, no. 2 (2017): 275-294.