Inference for QTL Hotspots
Add phenotypes to cross object.
Perform CMST Tests on cross object
Summary of threshold results
Get genetic information on candidate regulators and co-mapping traits.
Get common QTLs for phenotypes
Pull high LOD values with chr and pos.
Conduct NL and N permutation tests
Hotspot size routines.
Code for parallelizing R/qtlhot.
Determine false positive and true positive rates for known targets.
Wrapper routine for simulations.
Simulate Cross for Causal Tests
Conduct West-Wu (Q) permutation tests
Functions to infer co-mapping trait hotspots and causal models. Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365. <doi:10.1534/genetics.112.139451>. Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013) Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013. <doi:10.1534/genetics.112.147124>.