Generate knockoffs for genetic data and hidden Markov models.
  For more information, see the website below and the accompanying papers: 
  "Gene hunting with hidden Markov model knockoffs", Sesia et al., Biometrika, 2019, (<doi:10.1093/biomet/asy033>).
  "Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, (<doi:10.1101/631390>).

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.