Inference for QTL Hotspots
Add phenotypes to cross object.
Perform CMST Tests on cross object
Summary of threshold results
Determine false positive and true positive rates for known targets.
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.
Generate hotspots for the simulated examples in the manuscript.
neqtl.R Ported from http://github.com/kbroman/neqtl
Code for parallelizing R/qtlhot.
Compute Precision, True Positives, and False Positives
Compute Quantiles of High LOD Scores
Compute Quantiles for Hotperm Results
Wrapper routine for simulations.
Generates a "null dataset" cross
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>.