Introduction | Converting a Variant Call Format (VCF) file | Applying methods to subsets of data | Examples | Transition/transversion ratio | Heterozygosity | Principal Component Analysis | Hardy-Weinberg Equilibrium | Mendelian errors | Association tests

Introduction | Block iterators | Range iterators | Window iterators | List iterators

Overview | Convert VCF to GDS | Create a SeqVarData object | Population structure and relatedness | KING | PC-AiR | PC-Relate | Association tests | Null model | Single variant tests | Aggregate tests | References

Overview | Creating the SNP Annotation Data Object | Creating the Scan Annotation Data Object | Creating the Data Files | Genotype Files | Creating the Genotype file | Intensity Files | Creating the quality file | Creating the Intensity file | BAlleleFrequency and LogRRatio Files | Creating the BAlleleFrequency and LogRRatio file

Overview | Data | Preparing Scan Annotation Data | Reading in Genotype Data | R Matrix | GDS files | PLINK files | HapMap Data | Reading in the GRM from PC-Relate | Mixed Model Association Testing | Fit the Null Model | Quantitative Phenotypes | Multiple Fixed Effect Covariates | Multiple Random Effects | Heterogeneous Residual Variances | Binary Phentoypes | Run SNP-Phenotype Association Tests | Output | The Null Model | The Association Tests | Heritability Estimation | References

Overview | Principal Components Analysis in Related Samples (PC-AiR) | Relatedness Estimation Adjusted for Principal Components (PC-Relate) | Data | Reading in Genotype Data | R Matrix | GDS files | PLINK files | HapMap Data | LD pruning | Pairwise Measures of Ancestry Divergence | Running PC-AiR | Reference Population Samples | Partition a Sample without Running PCA | Output from PC-AiR | Plotting PC-AiR PCs | Running PC-Relate | Output from PC-Relate | References

1 Genotype data formats | 2 Annotation | 3 Input | 4 Output

1 Overview | 2 Preparing Data | 3 Batch Quality Checks | 4 Sample Quality Checks | 5 Sample Identity Checks | 6 Case-Control Confounding | 7 Chromosome Anomaly Detection | 8 SNP Quality Checks | 9 Preliminary Association Tests | 10 Acknowledgements