# Inference for QTL Hotspots

## Documentation for package ‘qtlhot’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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