Package: ldsep 2.1.6

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.zip(r-4.7)ldsep_2.1.6.zip(r-4.6)ldsep_2.1.6.zip(r-4.5)
ldsep_2.1.6.tgz(r-4.6-x86_64)ldsep_2.1.6.tgz(r-4.6-arm64)ldsep_2.1.6.tgz(r-4.5-x86_64)ldsep_2.1.6.tgz(r-4.5-arm64)
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✨
DESCRIPTION |NEWS
card.svg |card.png
ldsep/json (API)

# Install 'ldsep' in R:
install.packages('ldsep', repos = c('https://dcgerard.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

5.52 score 11 stars 30 scripts 271 downloads 16 exports 33 dependencies

Last updated from:14b2be97c8. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK223
linux-devel-x86_64OK223
source / vignettesOK326
linux-release-arm64OK251
linux-release-x86_64OK210
macos-release-arm64OK117
macos-release-x86_64OK284
macos-oldrel-arm64OK117
macos-oldrel-x86_64OK282
windows-develOK228
windows-releaseOK255
windows-oldrelOK182
wasm-releaseOK191

Exports:Dprimeformat_lddfget_prob_arraygl_to_gpis.lddfldestldest_compldest_hapldfastldshrinkmldestpbnorm_distpvcalcslcorsldestzshrink

Dependencies:abindashrclueclustercodetoolscorrplotdoParalleletrunctfBasicsforeachgssinvgammairlbaiteratorslatticelpSolveMASSMatrixmatrixStatsmixsqpmodeestRcppRcppArmadillormutilrpartspatialSQUAREMstablestablediststatiptimeDatetimeSeriestruncnorm

LD Estimation Pipeline from VCF
Summary | Analysis | Extract data from a VCF file using VariantAnnotation | Genotype individuals using updog | Extracting Log-likelihoods using fitPoly | Estimate LD using ldsep | References
Rendered fromvcf.Rmdusingknitr::rmarkdown

Last update: 2025-09-18
Started: 2020-10-23

Fast LD Estimation
Abstract | Analysis | References
Rendered fromfast.Rmdusingknitr::rmarkdown

Last update: 2025-09-17
Started: 2020-09-14