Package: bqtl 1.0-38

Charles C. Berry

bqtl: Bayesian QTL Mapping Toolkit

QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools.

Authors:Charles C. Berry [aut, cre]

bqtl_1.0-38.tar.gz
bqtl_1.0-38.tar.gz(r-4.5-noble)bqtl_1.0-38.tar.gz(r-4.4-noble)
bqtl_1.0-38.tgz(r-4.4-emscripten)bqtl_1.0-38.tgz(r-4.3-emscripten)
bqtl.pdf |bqtl.html✨
bqtl/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
Datasets:

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

1.57 score 18 scripts 1.0k downloads 28 exports 0 dependencies

Last updated 2 months agofrom:cb7fa78d3a. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-linux-x86_64OKOct 25 2024

Exports:bc1.levelsbqtlbqtl.fitterconfigsf2.levelslapadjlinear.bayeslocuslogliklogpostmake.analysis.objmake.map.framemake.regressor.matrixmake.state.matrixmake.varcovmap.indexmap.locmap.locationmap.namesmarker.fillplot.map.frameposteriorri.levelsswapswapbc1swapf2twohkvarcov

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Some Introductory Commentsbqtl-package
Use Laplace Approximations to improve linear approximations to the posterioradjust.linear.bayes
Bayesian QTL Model Fittingbqtl
Internal BQTL functions%equiv% map.dx rhs.bqtl uniq.config version.bqtl zero.dup
Get loglikelihoods for many models of a common formbqtl.fitter
Extract Coefficients from fitted objectscoef.bqtl coef.bqtl.list
Lookup loci or effects for genetic model formulasconfigs
Treat locus as covariatecovar
Extract formula from bqtl objectformula.bqtl
Approximate marginal posterior for chosen modellapadj
Bayesian QTL mapping via Linearized Likelihoodlinear.bayes
A simulated datasetlittle.ana.bc
A simulated datasetlittle.ana.f2
Simulated Marker Datalittle.bc.markers
Simulated Phenotype Datalittle.bc.pheno
Simulated Marker Datalittle.f2.markers
Simulated Phenotype Datalittle.f2.pheno
Marker Map Description for Simulated Datalittle.map.dx
Package of Simulated Marker Map Informationlittle.map.frame
Package of Simulated Marker Map Informationlittle.mf.5
Lookup loci or effects for genetic model formulasadd dom locus
Extract loglikelihood, log posterior, or posterior from fitted modelsloglik loglik.bqtl loglik.bqtl.list loglik.default logpost logpost.bqtl logpost.bqtl.list logpost.default posterior posterior.bqtl posterior.bqtl.list posterior.default
Set up data for QTL mappingmake.analysis.obj
Keep track of fully informative markers or statesmake.loc.right
Provide a default priormake.location.prior
Create marker map specificationsmake.map.frame
Translate a marker.frame.object to numeric matrixmake.marker.numeric
Create regressors using expected marker valuesmake.regressor.matrix
Create state.matrix.objectmake.state.matrix
Create moment matricesmake.varcov
Look up numerical index(es) of map locationsmap.index map.index.analysis.object map.index.default
Report map locationmap.loc map.location map.location.analysis.object map.location.bqtl map.location.bqtl.list map.location.default
Look up names of markers or locimap.names map.names.analysis.object map.names.bqtl map.names.bqtl.list map.names.default map.names.map.frame
Map Positions Between Markersmarker.fill
Define marker level codesbc1.levels f2.levels marker.levels ri.levels
plots by chromosome locationplot.analysis.object plot.map.frame
fitted values from QTL modelsfitted.bqtl predict.bqtl
Residuals or Predicted Values for linear.bayes objectsfitted.linear.bayes predict.linear.bayes residuals.linear.bayes
Residuals from QTL modelsresiduals.bqtl
Summarize Laplace approximationssummary.adj
Summarize bqtl objectsummary.bqtl
Summary methods for basic data objectssummary.analysis.object summary.map.frame
Summarize Gibbs samples for a k-gene modelsummary.swap
MCMC sampling of multigene modelsswap
Sample BC1 or Recombinant Inbred loci via approximate posterior.swapbc1
Sample F2 loci via approximate posteriorswapf2
One and Two Gene Models Using Linearized Posteriortwohk
One and Two Gene Models Using Linearized Posteriortwohkbc1 twohkf2
Create moment matricesvarcov