Package: pould
Title: Phased or Unphased Linkage Disequilibrium
Version: 1.0.2
Authors@R: person("Steven", "Mack", email = "steven.mack@ucsf.edu", role = c("aut", "cre"))
Description: 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>.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
Imports:
        haplo.stats,gap,stats,utils,ggplot2,reshape2,BIGDAWG,graphics,stringr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-04-29 00:54:36 UTC; sjmack
Author: Steven Mack [aut, cre]
Maintainer: Steven Mack <steven.mack@ucsf.edu>
Repository: CRAN
Date/Publication: 2026-05-01 16:40:02 UTC
Built: R 4.6.0; ; 2026-05-01 20:20:31 UTC; unix
