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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:799ad16ceb. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-linux-x86_64 | OK | Aug 28 2024 |
Exports:add.phenosbig.phase0CMSTtestsCMSTtestsListfilter.thresholdFitAllTestsGetCandRegGetCisCandRegGetCoMappingTraitsGetCommonQtlshighlodhotpermhotsizeinclude.hotspotsJoinTestOutputsp.adjust.npparallel.qtlhotPrecTpFpMatrixpull.highlodqtlhot.phase0sim.null.crosssim.null.pheno.dataSimCrossCausalww.perm
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add phenotypes to cross object. | add.phenos |
| Perform CMST Tests on cross object | CMSTtests CMSTtestsList |
| Summary of threshold results | filter.threshold |
| Get genetic information on candidate regulators and co-mapping traits. | GetCandReg GetCisCandReg GetCoMappingTraits |
| Get common QTLs for phenotypes | GetCommonQtls |
| 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 tests | hotperm 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 Tests | CMSTCross SimCrossCausal SimCrossIndep |
| Conduct West-Wu (Q) permutation tests | print.ww.perm summary.ww.perm ww.perm |