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) .


Reference manual

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1.0.1 by Steven Mack, a year ago

Browse source code at

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