pould: Phased or Unphased Linkage Disequilibrium

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>.

Version: 1.0.1
Depends: R (≥ 3.5.0)
Imports: haplo.stats, gap, stats, utils, ggplot2, reshape2, BIGDAWG, graphics
Suggests: knitr, rmarkdown
Published: 2020-10-16
Author: Steven Mack [aut, cre]
Maintainer: Steven Mack <steven.mack at ucsf.edu>
License: GPL (≥ 3)
NeedsCompilation: no
Materials: README NEWS
CRAN checks: pould results


Reference manual: pould.pdf
Vignettes: Using pould
Package source: pould_1.0.1.tar.gz
Windows binaries: r-devel: pould_1.0.1.zip, r-release: pould_1.0.1.zip, r-oldrel: pould_1.0.1.zip
macOS binaries: r-release: pould_1.0.1.tgz, r-oldrel: pould_1.0.1.tgz
Old sources: pould archive


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