| add.phenos | Add phenotypes to cross object. | 
| big.phase0 | Code for parallelizing R/qtlhot. | 
| CitTests | Determine false positive and true positive rates for known targets. | 
| CMSTCross | Simulate Cross for Causal Tests | 
| CMSTtests | Perform CMST Tests on cross object | 
| CMSTtestsList | Perform CMST Tests on cross object | 
| filter.threshold | Summary of threshold results | 
| FitAllTests | Determine false positive and true positive rates for known targets. | 
| GetCandReg | Get genetic information on candidate regulators and co-mapping traits. | 
| GetCisCandReg | Get genetic information on candidate regulators and co-mapping traits. | 
| GetCoMappingTraits | Get genetic information on candidate regulators and co-mapping traits. | 
| GetCommonQtls | Get common QTLs for phenotypes | 
| highlod | Pull high LOD values with chr and pos. | 
| hotperm | Conduct NL and N permutation tests | 
| hotperm1 | Conduct NL and N permutation tests | 
| hotsize | Hotspot size routines. | 
| hotsize.highlod | Hotspot size routines. | 
| hotsize.scanone | Hotspot size routines. | 
| include.hotspots | Wrapper routine for simulations. | 
| JoinTestOutputs | Determine false positive and true positive rates for known targets. | 
| max.highlod | Pull high LOD values with chr and pos. | 
| mySimulations | Wrapper routine for simulations. | 
| p.adjust.np | Determine false positive and true positive rates for known targets. | 
| parallel.qtlhot | Code for parallelizing R/qtlhot. | 
| plot.highlod | Pull high LOD values with chr and pos. | 
| plot.hotsize | Hotspot size routines. | 
| PrecTpFpMatrix | Determine false positive and true positive rates for known targets. | 
| print.highlod | Pull high LOD values with chr and pos. | 
| print.hotperm | Conduct NL and N permutation tests | 
| print.hotsize | Hotspot size routines. | 
| print.summary.hotperm | Conduct NL and N permutation tests | 
| print.ww.perm | Conduct West-Wu (Q) permutation tests | 
| pull.highlod | Pull high LOD values with chr and pos. | 
| qtlhot.phase0 | Code for parallelizing R/qtlhot. | 
| quantile.highlod | Pull high LOD values with chr and pos. | 
| quantile.hotperm | Conduct NL and N permutation tests | 
| sim.hotspot | Wrapper routine for simulations. | 
| sim.null.cross | Wrapper routine for simulations. | 
| sim.null.pheno.data | Wrapper routine for simulations. | 
| SimCrossCausal | Simulate Cross for Causal Tests | 
| SimCrossIndep | Simulate Cross for Causal Tests | 
| summary.highlod | Pull high LOD values with chr and pos. | 
| summary.hotperm | Conduct NL and N permutation tests | 
| summary.hotsize | Hotspot size routines. | 
| summary.ww.perm | Conduct West-Wu (Q) permutation tests | 
| ww.perm | Conduct West-Wu (Q) permutation tests |