Other packages > Find by keyword >

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 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:52), 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)
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

PCADSC  
Tools for Principal Component Analysis-Based Data Structure Comparisons
A suite of non-parametric, visual tools for assessing differences in data structures for two datase ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
Download / Learn more Package Citations See dependency  
clinUtils  
General Utility Functions for Analysis of Clinical Data
Utility functions to facilitate the import, the reporting and analysis of clinical data. Example ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA