Package: snplinkage
Title: Single Nucleotide Polymorphisms Linkage Disequilibrium
        Visualizations
Version: 1.2.0
Authors@R: c(
  person("Thomas", "Charlon", role = c("aut", "cre"), email = "charlon@protonmail.com", comment = c(ORCID = "0000-0001-7497-0470")),
  person("Karl", "Forner", role = "aut"),
  person("Alessandro", "Di Cara", role = "aut"),
  person("Jérôme", "Wojcik", role = "aut"))
Description: Linkage disequilibrium visualizations of up to several
        hundreds of single nucleotide polymorphisms (SNPs), annotated
        with chromosomic positions and gene names. Two types of plots
        are available for small numbers of SNPs (<40) and for large
        numbers (tested up to 500). Both can be extended by combining
        other ggplots, e.g. association studies results, and functions
        enable to directly visualize the effect of SNP selection
        methods, as minor allele frequency filtering and TagSNP
        selection, with a second correlation heatmap. The SNPs
        correlations are computed on Genotype Data objects from the
        'GWASTools' package using the 'SNPRelate' package, and the
        plots are customizable 'ggplot2' and 'gtable' objects and are
        annotated using the 'biomaRt' package. Usage is detailed in the
        vignette with example data and results from up to 500 SNPs of
        1,200 scans are in Charlon T. (2019)
        <doi:10.13097/archive-ouverte/unige:161795>.
Imports: biomaRt, cowplot, data.table, gdsfmt, ggplot2, ggrepel, grid,
        grDevices, gtable, knitr, magrittr, methods, parallel,
        reshape2, SNPRelate, stats, utils
Depends: R (>= 4.1.0), GWASTools (>= 1.10.1)
Suggests: rmarkdown, testthat
biocViews: GeneticVariability, MicroArray, SNP
URL: https://gitlab.com/thomaschln/snplinkage
BugReports: https://gitlab.com/thomaschln/snplinkage/-/issues
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libxml2-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: https://thomaschln.r-universe.dev
Date/Publication: 2025-04-22 20:28:14 UTC
RemoteUrl: https://gitlab.com/thomaschln/snplinkage
RemoteRef: HEAD
RemoteSha: bd8604c9e266ac0f26feed832accaae047964862
NeedsCompilation: no
Packaged: 2026-06-19 08:47:08 UTC; root
Author: Thomas Charlon [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7497-0470>),
  Karl Forner [aut],
  Alessandro Di Cara [aut],
  Jérôme Wojcik [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>