Inference for QTL Hotspots

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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