Linkage Disequilibrium Shrinkage Estimation for Polyploids [R package ldsep version 2.1.6]

David Gerard

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: 2.1.6

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: 2025年09月18日

DOI: 10.32614/CRAN.package.ldsep

Author: David Gerard ORCID iD [aut, cre]

Maintainer: David Gerard <gerard.1787 at gmail.com>

BugReports: https://github.com/dcgerard/ldsep/issues

License: GPL (≥ 3)

URL: https://dcgerard.github.io/ldsep/

NeedsCompilation: yes

Citation: ldsep citation info

Materials: README, NEWS

CRAN checks: ldsep results

Documentation:

Reference manual: ldsep.html , ldsep.pdf

Vignettes: Fast LD Estimation (source, R code)
LD Estimation Pipeline from VCF (source, R code)

Downloads:

Package source: ldsep_2.1.6.tar.gz

Windows binaries: r-devel: ldsep_2.1.6.zip, r-release: ldsep_2.1.6.zip, r-oldrel: ldsep_2.1.6.zip

macOS binaries: r-release (arm64): ldsep_2.1.6.tgz, r-oldrel (arm64): ldsep_2.1.6.tgz, r-release (x86_64): ldsep_2.1.6.tgz, r-oldrel (x86_64): ldsep_2.1.6.tgz

Old sources: ldsep archive

Linking:

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