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 |