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) , and Osoegawa et. al. (2019b) .


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install.packages("pould")

1.0.0 by Steven Mack, 4 months ago


Browse source code at https://github.com/cran/pould


Authors: Steven Mack [aut, cre]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports haplo.stats, gap, stats, utils, ggplot2, reshape2, BIGDAWG, graphics

Suggests knitr, rmarkdown


See at CRAN