Linkage Disequilibrium Shrinkage Estimation for Polyploids

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 main functions are ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink().


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1.0.0 by David Gerard, 3 months ago

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Authors: David Gerard [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports Rcpp, foreach, doParallel, ashr, corrplot, lpSolve

Suggests testthat, covr, knitr, rmarkdown, updog

Linking to Rcpp, RcppArmadillo

See at CRAN