Package: ldsep 2.1.7

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
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ldsep_2.1.7.tgz(r-4.6-x86_64)ldsep_2.1.7.tgz(r-4.6-arm64)ldsep_2.1.7.tgz(r-4.5-x86_64)ldsep_2.1.7.tgz(r-4.5-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://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

5.59 score 13 stars 30 scripts 583 downloads 17 exports 19 dependencies

Last updated from:bbe3912cdc. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK206
linux-devel-x86_64OK226
source / vignettesOK326
linux-release-arm64OK167
linux-release-x86_64OK213
macos-release-arm64OK139
macos-release-x86_64OK255
macos-oldrel-arm64OK152
macos-oldrel-x86_64OK616
windows-devel-arm64OK294
windows-devel-x86_64OK259
windows-release-arm64OK382
windows-release-x86_64OK205
windows-oldrel-x86_64OK212
wasm-releaseOK151

Exports:Dprimeformat_lddfget_prob_arraygl_to_gphsmis.lddfldestldest_compldest_hapldfastldshrinkmldestpbnorm_distpvcalcslcorsldestzshrink

Dependencies:abindashrcodetoolscorrplotdoParalleletrunctforeachinvgammairlbaiteratorslatticelpSolveMatrixmatrixStatsmixsqpRcppRcppArmadilloSQUAREMtruncnorm

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