Package: qtlhot 1.2.10

Brian S. Yandell

qtlhot: Inference for QTL Hotspots

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>.

Authors:Elias Chaibub Neto [aut], Brian S Yandell [aut], Brian S. Yandell [cre]

qtlhot_1.2.10.tar.gz
qtlhot_1.2.10.zip(r-4.7-any)qtlhot_1.2.10.zip(r-4.6-any)qtlhot_1.2.10.zip(r-4.5-any)
qtlhot_1.2.10.tgz(r-4.6-any)qtlhot_1.2.10.tgz(r-4.5-any)
qtlhot_1.2.10.tar.gz(r-4.7-any)qtlhot_1.2.10.tar.gz(r-4.6-any)
qtlhot_1.2.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
qtlhot/json (API)

# Install 'qtlhot' in R:
install.packages('qtlhot', repos = c('https://byandell-sysgen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/byandell-sysgen/qtlhot/issues

Datasets:

On CRAN:

Conda:

5.58 score 3 stars 42 scripts 289 downloads 1 mentions 21 exports 21 dependencies

Last updated from:eb8fe508bd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK113
source / vignettesOK192
linux-releaseOK156
macos-releaseOK163
macos-oldrelOK195
windows-develOK80
windows-releaseOK86
windows-oldrelOK69
wasm-releaseOK103

Exports:CitTestsCMSTtestsCMSTtestsListCombineTestsFitAllTestsGetCandRegGetCisCandRegGetCoMappingTraitsGetCommonQtlshighlodhotpermhotsizeinclude.hotspotsJoinTestOutputsneqtlPrecTpFpMatrixpull.highlodquantile_highlodquantile_hotpermsim.null.crossSimCrossCausal

Dependencies:bromanclicorpcorcpp11farverggplot2gluegtableisobandlabelinglifecyclemnormtqtlR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Qtlhot Tutorial
Motivation | Overview | Basic functionality with No Real Hotspots | Example with Uncorrelated Phenotypes | References
Rendered fromqtlhot.Rmdusingknitr::rmarkdown

Last update: 2025-12-09
Started: 2025-12-08

Causal Model Selection Hypothesis Tests in Systems Genetics: \ a tutorial
Motivation | Overview | Basic functionality | Other Functions | References
Rendered fromcmst.Rmdusingknitr::rmarkdown

Last update: 2025-12-09
Started: 2025-12-08

Readme and manuals

Help Manual

Help pageTopics
Add phenotypes to cross object.add.phenos
MST Sample Cross objectCMSTCross
Perform CMST Tests on cross objectCMSTtests CMSTtestsList GetCisCandReg
Summary of threshold resultsfilter.threshold
Determine false positive and true positive rates for known targets.CitTests CombineTests FitAllTests JoinTestOutputs
Get genetic information on candidate regulators and co-mapping traits.GetCandReg GetCoMappingTraits
Get common QTLs for phenotypesGetCommonQtls
Pull high LOD values with chr and pos.highlod max.highlod plot.highlod print.highlod pull.highlod summary.highlod
Conduct NL and N permutation testshotperm plot.hotperm print.hotperm print.summary.hotperm summary.hotperm
Hotspot Permutation Samplehotperm1
Hotspot size routines.hotsize hotsize.highlod hotsize.scanone max.hotsize plot.hotsize print.hotsize summary.hotsize
Generate hotspots for the simulated examples in the manuscript.include.hotspots
neqtl.R Ported from http://github.com/kbroman/neqtlneqtl
Code for parallelizing R/qtlhot.parallel.qtlhot
Compute Precision, True Positives, and False PositivesPrecTpFpMatrix
Compute Quantiles of High LOD Scoresquantile_highlod
Compute Quantiles for Hotperm Resultsquantile_hotperm
Wrapper routine for simulations.sim.hotspot
Generates a "null dataset" crosssim.null.cross
Simulate Cross for Causal TestsSimCrossCausal
Conduct West-Wu (Q) permutation testsprint.ww.perm summary.ww.perm ww.perm