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: 2026-07-04 02:02:09 UTC; root
Author: Steven Mack [aut, cre]
Maintainer: Steven Mack <steven.mack@ucsf.edu>
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libxml2-dev
        libssl-dev
Repository: https://sjmack.r-universe.dev
Date/Publication: 2026-05-01 19:45:48 UTC
RemoteUrl: https://github.com/cran/pould
RemoteRef: HEAD
RemoteSha: db952b3f1cb015418e1b714b398383722de9ecd5