Vignettes of package chopsticks

Example of genome-wide association testing:

Introduction to chopsticks for analysis of GWA studies

Comparing clustering algorithms:

Comparing clustering algorithms for Illumina platforms

Imputed SNP analyses and meta-analysis with chopsticks:

Imputation and meta-analysis with chopsticks

PCA vignette:

Principal components analysis with chopsticks

TDT vignette:

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Initial paper in "Human Heredity" (now rather out of date, but it describes the philosophy of the package)