# Inference for QTL Hotspots

## Documentation for package ‘qtlhot’ version 1.2.10

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

## Help Pages

add.phenos | Add phenotypes to cross object.
CitTests | Determine false positive and true positive rates for known targets.
CMSTCross | MST Sample Cross object
CMSTtests | Perform CMST Tests on cross object
CMSTtestsList | Perform CMST Tests on cross object
CombineTests | Determine false positive and true positive rates for known targets.
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 | Perform CMST Tests on cross object
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 | Hotspot Permutation Sample
hotsize | Hotspot size routines.
hotsize.highlod | Hotspot size routines.
hotsize.scanone | Hotspot size routines.
include.hotspots | Generate hotspots for the simulated examples in the manuscript.
JoinTestOutputs | Determine false positive and true positive rates for known targets.
max.highlod | Pull high LOD values with chr and pos.
max.hotsize | Hotspot size routines.
neqtl | neqtl.R Ported from http://github.com/kbroman/neqtl
parallel.qtlhot | Code for parallelizing R/qtlhot.
plot.highlod | Pull high LOD values with chr and pos.
plot.hotperm | Conduct NL and N permutation tests
plot.hotsize | Hotspot size routines.
PrecTpFpMatrix | Compute Precision, True Positives, and False Positives
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.
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
SimCrossCausal | 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