Inference for QTL Hotspots

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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