Licensing | Citing | Introduction | Installation | Using RAIDS: step-by-step explanation | Step 1. Set-up working directory and provide population reference files | 1.1 Create a working directory structure | 1.2 Download the population reference files | Step 2 Ancestry inference with RAIDS | 2.1 Set-up the required directories | 2.2 Sample the reference data for donors whose genotypes will be used for synthesis and optimize ancestry inference parameters using synthetic data | 2.3 Infer ancestry | Step 3. Examine the value of the inference call | 3.1 Inspect the inference and the optimal parameters | 3.2 Visualize the RAIDS performance for the synthetic data | Format population reference dataset (optional) | Session info | References

Main Steps | Main Step - Ancestry Inference | DNA Data - Wrapper function to run ancestry inference on DNA data | Population reference files | Profile SNP file | Profile PED RDS file | Example | RNA data - Wrapper function to run ancestry inference on RNA data | Format population reference dataset (optional) | Session info | References

Population Reference GDS File | Population Reference Annotation GDS file | Pre-processed files, from 1000 Genomes in hg38, are available | Session info | References

Licensing | Citing | Introduction | Loading methInheritSim package | Description of the simulation process | Simulated control dataset | Simulated case dataset | Case study | The simulated dataset | The simulation | Files generated by the simulation | Synthetic chromosome in GRanges format ("syntheticChr" prefix) | Simulation information in GRanges format ("simData" prefix) | Information about DMS state ("stateDiff" prefix) | Files related to saveGRanges parameter | Raw methylation data for all samples in GRanges format ("methylGR" prefix) | Information about controls and cases ("treatment" prefix) | Files related to saveMethylKit parameter | Raw methylation data in methylRaw format ("methylObj" prefix) | Files related to runAnalysis parameter | Methylation events present in multiple samples in methylBase format ("meth" prefix) | Differential methylation statistics in methylDiff format ("methDiff" prefix) | Conclusion