CMSTCross               MST Sample Cross object
CMSTtests               Perform CMST Tests on cross object
FitAllTests             Determine false positive and true positive
                        rates for known targets.
GetCandReg              Get genetic information on candidate regulators
                        and co-mapping traits.
GetCommonQtls           Get common QTLs for phenotypes
PrecTpFpMatrix          Compute Precision, True Positives, and False
                        Positives
SimCrossCausal          Simulate Cross for Causal Tests
add.phenos              Add phenotypes to cross object.
filter.threshold        Summary of threshold results
highlod                 Pull high LOD values with chr and pos.
hotperm                 Conduct NL and N permutation tests
hotperm1                Hotspot Permutation Sample
hotsize                 Hotspot size routines.
include.hotspots        Generate hotspots for the simulated examples in
                        the manuscript.
neqtl                   neqtl.R Ported from
                        http://github.com/kbroman/neqtl
parallel.qtlhot         Code for parallelizing R/qtlhot.
quantile_highlod        Compute Quantiles of High LOD Scores
quantile_hotperm        Compute Quantiles for Hotperm Results
sim.hotspot             Wrapper routine for simulations.
sim.null.cross          Generates a "null dataset" cross
ww.perm                 Conduct West-Wu (Q) permutation tests
