ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

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 main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.

Version: 2.1.5
Depends: R (≥ 2.10)
Imports: Rcpp, foreach, doParallel, ashr, corrplot, lpSolve, abind, modeest, matrixStats
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, covr, knitr, rmarkdown, updog (≥ 2.0.2), VariantAnnotation
Published: 2022-10-18
DOI: 10.32614/CRAN.package.ldsep
Author: David Gerard ORCID iD [aut, cre]
Maintainer: David Gerard <gerard.1787 at>
License: GPL-3
NeedsCompilation: yes
Citation: ldsep citation info
Materials: README NEWS
CRAN checks: ldsep results


Reference manual: ldsep.pdf
Vignettes: Fast LD Estimation
LD Estimation Pipeline from VCF


Package source: ldsep_2.1.5.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): ldsep_2.1.5.tgz, r-oldrel (arm64): ldsep_2.1.5.tgz, r-release (x86_64): ldsep_2.1.5.tgz, r-oldrel (x86_64): ldsep_2.1.5.tgz
Old sources: ldsep archive


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