Package: ldsep 2.1.7

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_2.1.7.tar.gz
ldsep_2.1.7.zip(r-4.7-x86_64)ldsep_2.1.7.zip(r-4.7-arm64)ldsep_2.1.7.zip(r-4.6-x86_64)ldsep_2.1.7.zip(r-4.6-arm64)
ldsep_2.1.7.tar.gz(r-4.7-arm64)ldsep_2.1.7.tar.gz(r-4.7-x86_64)ldsep_2.1.7.tar.gz(r-4.6-arm64)ldsep_2.1.7.tar.gz(r-4.6-x86_64)
ldsep_2.1.7.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://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 428 downloads 17 exports 19 dependencies

Last updated from:bb8164e47f. Checks:10 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK155
linux-devel-x86_64OK204
source / vignettesOK337
linux-release-arm64OK190
linux-release-x86_64OK200
windows-devel-arm64OK314
windows-devel-x86_64OK231
windows-release-arm64OK258
windows-release-x86_64OK138
wasm-releaseOK171

Exports:Dprimeformat_lddfget_prob_arraygl_to_gphsmis.lddfldestldest_compldest_hapldfastldshrinkmldestpbnorm_distpvcalcslcorsldestzshrink

Dependencies:abindashrcodetoolscorrplotdoParalleletrunctforeachinvgammairlbaiteratorslatticelpSolveMatrixmatrixStatsmixsqpRcppRcppArmadilloSQUAREMtruncnorm

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

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

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: 2020-11-14