Simulated Power Analysis in the Realized Collaborative Cross
This package provides two primary functions:
- Simulate Collaborative Cross (CC) phenotype data from the actual CC lines
- Potential parameters:
- QTL effect size
- Overall strain effect size
- Number of CC lines
- Number of replicates
- Number of functional alleles at the QTL
- Strain distribution pattern of the functional alleles
- Estimate power based on rapid genome scans of simulated data
- Genome scans are highly optimized by storing QR decompositions when appropriate
- Signicance thresholds determined through rapid permutations
- Additional statistics of interest possible, such as false positive rate
Finally, sparcc also includes functionality to visualize results. It can also be extended to other recombinant inbred line (RIL) panels.