Single Nucleotide Polymorphism Linkage Disequilibrium Visualizations (CRAN, 2023)

Single nucleotide polymorphisms are the most common genetic variations in humans and genome-wide microarrays measure up to several millions. Physically close polymorphisms often exhibit correlation structures and are said to be in linkage disequilibrium when they are more correlated than randomly expected. The snplinkage package provides linkage disequilibrium visualizations by displaying correlation matrices annotated with chromosomic positions and gene names. Two types of displays are provided to focus on small or large regions, and both can be extended to combine associations results or investigate feature selection methods. This article introduces the package and illustrates the variety of correlation structures found genome-wide by focusing on 3 regions associated with autoimmune diseases: the chromosome 1 region 1p13.2 (111-115 Mbp), the chromosome 8 region 8p23.1 (7-12 Mbp) and the chromosome 6 region 6p21.3 (29-35 Mbp).