Package: qtlhot 1.0.4

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 <[email protected]> and Brian S Yandell <[email protected]>

qtlhot_1.0.4.tar.gz
qtlhot_1.0.4.tar.gz(r-4.5-noble)qtlhot_1.0.4.tar.gz(r-4.4-noble)
qtlhot_1.0.4.tgz(r-4.4-emscripten)qtlhot_1.0.4.tgz(r-4.3-emscripten)
qtlhot.pdf |qtlhot.html✨
qtlhot/json (API)

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

Peer review:

Datasets:
  • CMSTCross - Simulate Cross for Causal Tests
  • hotperm1 - Conduct NL and N permutation tests

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.78 score 30 scripts 218 downloads 1 mentions 24 exports 3 dependencies

Last updated 7 years agofrom:799ad16ceb. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-linux-x86_64OKNov 26 2024

Exports:add.phenosbig.phase0CMSTtestsCMSTtestsListfilter.thresholdFitAllTestsGetCandRegGetCisCandRegGetCoMappingTraitsGetCommonQtlshighlodhotpermhotsizeinclude.hotspotsJoinTestOutputsp.adjust.npparallel.qtlhotPrecTpFpMatrixpull.highlodqtlhot.phase0sim.null.crosssim.null.pheno.dataSimCrossCausalww.perm

Dependencies:corpcormnormtqtl

CMST Tutorial

Rendered fromcmst.Rnwusingutils::Sweaveon Nov 26 2024.

Last update: 2012-11-07
Started: 2012-09-17

Qtlhot Tutorial

Rendered fromqtlhot.Rnwusingutils::Sweaveon Nov 26 2024.

Last update: 2018-04-05
Started: 2012-05-30

Readme and manuals

Help Manual

Help pageTopics
Add phenotypes to cross object.add.phenos
Perform CMST Tests on cross objectCMSTtests CMSTtestsList
Summary of threshold resultsfilter.threshold
Get genetic information on candidate regulators and co-mapping traits.GetCandReg GetCisCandReg GetCoMappingTraits
Get common QTLs for phenotypesGetCommonQtls
Pull high LOD values with chr and pos.highlod max.highlod plot.highlod print.highlod pull.highlod quantile.highlod summary.highlod
Conduct NL and N permutation testshotperm hotperm1 print.hotperm print.summary.hotperm quantile.hotperm summary.hotperm
Hotspot size routines.hotsize hotsize.highlod hotsize.scanone plot.hotsize print.hotsize summary.hotsize
Code for parallelizing R/qtlhot.big.phase0 parallel.qtlhot qtlhot.phase0
Determine false positive and true positive rates for known targets.CitTests FitAllTests JoinTestOutputs p.adjust.np PrecTpFpMatrix
Wrapper routine for simulations.include.hotspots mySimulations sim.hotspot sim.null.cross sim.null.pheno.data
Simulate Cross for Causal TestsCMSTCross SimCrossCausal SimCrossIndep
Conduct West-Wu (Q) permutation testsprint.ww.perm summary.ww.perm ww.perm