Vignettes of package snpMatrix

Example of genome-wide association testing:

Introduction to snpMatrix for analysis of GWA studies

Comparing clustering algorithms:

Comparing clustering algorithms for Illumina platforms

Imputed SNP analyses and meta-analysis with snpMatrix:

Imputation and meta-analysis with snpMatrix

PCA vignette:

Principal components analysis with snpMatrix

snpStats Bugs:

Catalogs of Bugs in current Bioc snpMatrix/snpStats

TDT vignette:

Use of snpMatrix in family--based association studies

An R package for analysis of whole-genome association studies:

Initial paper in "Human Heredity" (now rather out of date, but it describes the philosophy of the package)