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>.

A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example to export to a PLINK set.

Tools for performing variable selection in three-way data using N-PLS 
    in combination with L1 penalization, Selectivity Ratio and VIP scores. 
    The N-PLS model (Rasmus Bro, 1996 <DOI:10.1002/(SICI)1099-128X(199601)10:1%3C47::AID-CEM400%3E3.0.CO;2-C>) 
    is the natural extension of PLS (Partial Least Squares) to N-way structures, and tries 
    to maximize the covariance between X and Y data arrays. The package also adds
    variable selection through L1 penalization, Selectivity Ratio and VIP scores.

Three functions to clean, summarize and prepare genomic datasets to Genome
    Selection and Genome Association analysis and to estimate population genetic parameters.

The goal of 'snpsettest' is to provide simple tools that perform
             set-based association tests (e.g., gene-based association tests)
             using GWAS (genome-wide association study) summary statistics. A
             set-based association test in this package is based on the
             statistical model described in VEGAS (versatile gene-based
             association study), which combines the effects of a set of SNPs
             accounting for linkage disequilibrium between markers. This package
             uses a different approach from the original VEGAS implementation to
             compute set-level p values more efficiently, as described in
             <https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.