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ldsep  

Linkage Disequilibrium Shrinkage Estimation for Polyploids
View on CRAN: Click here


Download and install ldsep package within the R console
Install from CRAN:
install.packages("ldsep")

Install from Github:
library("remotes")
install_github("cran/ldsep")

Install by package version:
library("remotes")
install_version("ldsep", "2.1.6")



Attach the package and use:
library("ldsep")
Maintained by
David Gerard
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-08-02
Latest Update: 2022-10-18
Description:
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) and Gerard (2021b) .
How to cite:
David Gerard (2020). ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids. R package version 2.1.6, https://cran.r-project.org/web/packages/ldsep. Accessed 18 Sep. 2026.
Previous versions and publish date:
(2026-09-09 22:40), 1.0.0 (2020-08-02 03:20), 1.1.0 (2020-11-14 15:20), 2.0.1 (2021-02-12 16:30), 2.0.2 (2021-02-17 10:00), 2.1.0 (2021-06-11 20:00), 2.1.2 (2021-08-10 15:50), 2.1.4 (2022-02-11 16:00), 2.1.5 (2022-10-19 00:52), 2.1.6 (2025-09-18 19:10)
Other packages that cited ldsep R package
View ldsep citation profile
Other R packages that ldsep depends, imports, suggests or enhances
Complete documentation for ldsep
Functions, R codes and Examples using the ldsep R package
Some associated functions: Dprime . format_lddf . get_prob_array . gl_to_gp . glike . gp . is.lddf . ldest . ldest_comp . ldest_hap . ldfast . ldsep-package . ldshrink . mldest . pbnorm_dist . plot.lddf . pvcalc . slcor . sldest . uit . zshrink . 
Some associated R codes: RcppExports.R . data.R . fast.R . generics.R . ldgeno.R . ldsep-package.R . maxd.R . mds.R . mom.R . multild.R . sliding_window.R .  Full ldsep package functions and examples
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