README.md

In gkeele/sparcc: Simulated Power Analysis in the Realized Collaborative Cross

sparcc

Simulated Power Analysis in the Realized Collaborative Cross

This package provides two primary functions:

1. Simulate Collaborative Cross (CC) phenotype data from the actual CC lines
2. Potential parameters:
3. QTL effect size
4. Overall strain effect size
5. Number of CC lines
6. Number of replicates
7. Number of functional alleles at the QTL
8. Strain distribution pattern of the functional alleles
9. Estimate power based on rapid genome scans of simulated data
10. Genome scans are highly optimized by storing QR decompositions when appropriate
11. Signicance thresholds determined through rapid permutations
12. 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.

gkeele/sparcc documentation built on May 28, 2019, 5:43 a.m.