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qtlhot (version 1.0.4)

Inference for QTL Hotspots

Description

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. . 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. .

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Version

Install

install.packages('qtlhot')

Monthly Downloads

209

Version

1.0.4

License

GPL (>= 2)

Maintainer

Last Published

April 5th, 2018

Functions in qtlhot (1.0.4)

filter.threshold

Summary of threshold results
hotperm

Conduct NL and N permutation tests
SimCrossCausal

Simulate Cross for Causal Tests
PrecTpFpMatrix

Determine false positive and true positive rates for known targets.
add.phenos

Add phenotypes to cross object.
parallel.qtlhot

Code for parallelizing R/qtlhot.
sim.hotspot

Wrapper routine for simulations.
GetCommonQtls

Get common QTLs for phenotypes
highlod

Pull high LOD values with chr and pos.
hotsize

Hotspot size routines.
ww.perm

Conduct West-Wu (Q) permutation tests
GetCandReg

Get genetic information on candidate regulators and co-mapping traits.
CMSTtests

Perform CMST Tests on cross object