CRAN/E | pould

pould

Phased or Unphased Linkage Disequilibrium

Installation

About

Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) doi:10.1016/j.humimm.2019.01.010, and Osoegawa et. al. (2019b) doi:10.1016/j.humimm.2019.05.018.

Key Metrics

Version 1.0.1
R ≥ 3.5.0
Published 2020-10-16 1448 days ago
Needs compilation? no
License GPL (≥ 3)
CRAN checks pould results

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Maintainer

Maintainer

Steven Mack

Authors

Steven Mack

aut / cre

Material

README
NEWS
Reference manual
Package source

Vignettes

Using pould

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

pould archive

Depends

R ≥ 3.5.0

Imports

haplo.stats
gap
stats
utils
ggplot2
reshape2
BIGDAWG
graphics

Suggests

knitr
rmarkdown