Package: ldsep 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>.

Authors:David Gerard [aut, cre]

ldsep_2.1.6.tar.gz
ldsep_2.1.6.tar.gz(r-4.7-arm64)ldsep_2.1.6.tar.gz(r-4.7-x86_64)ldsep_2.1.6.tar.gz(r-4.6-arm64)ldsep_2.1.6.tar.gz(r-4.6-x86_64)
ldsep_2.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ldsep/json (API)
NEWS

# Install 'ldsep' in R:
install.packages('ldsep', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dcgerard/ldsep/issues

Pkgdown/docs site:https://dcgerard.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • glike - Genotype log-likelihoods from 'uit'
  • gp - Posterior probabilities from 'uit'
  • uit - Updog fits on the data from Uitdewilligen et. al.

On CRAN:

Conda:

openblascppopenmp

3.48 score 30 scripts 271 downloads 16 exports 33 dependencies

Last updated from:c17641ca42. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK203
linux-devel-x86_64OK189
source / vignettesOK340
linux-release-arm64OK215
linux-release-x86_64OK194
wasm-releaseOK193

Exports:Dprimeformat_lddfget_prob_arraygl_to_gpis.lddfldestldest_compldest_hapldfastldshrinkmldestpbnorm_distpvcalcslcorsldestzshrink

Dependencies:abindashrclueclustercodetoolscorrplotdoParalleletrunctfBasicsforeachgssinvgammairlbaiteratorslatticelpSolveMASSMatrixmatrixStatsmixsqpmodeestRcppRcppArmadillormutilrpartspatialSQUAREMstablestablediststatiptimeDatetimeSeriestruncnorm

Fast LD Estimation

David Gerard

Rendered fromfast.Rmdusingknitr::rmarkdownon Jun 15 2026.

Last update: 2025-09-18
Started: 2021-02-12

LD Estimation Pipeline from VCF

Rendered fromvcf.Rmdusingknitr::rmarkdownon Jun 15 2026.

Last update: 2025-09-18
Started: 2020-11-14