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bqtl (version 1.0-39)
Bayesian QTL Mapping Toolkit
Description
QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools.
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Install
install.packages('bqtl')
Monthly Downloads
488
Version
1.0-39
License
GPL (>= 2)
Maintainer
Charles C Berry
Last Published
December 14th, 2025
Functions in bqtl (1.0-39)
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little.map.frame
Package of Simulated Marker Map Information
little.ana.bc
A simulated dataset
make.map.frame
Create marker map specifications
little.ana.f2
A simulated dataset
make.location.prior
Provide a default prior
make.regressor.matrix
Create regressors using expected marker values
make.loc.right
Keep track of fully informative markers or states
little.mf.5
Package of Simulated Marker Map Information
locus
Lookup loci or effects for genetic model formulas
map.index
Look up numerical index(es) of map locations
make.varcov
Create moment matrices
marker.levels
Define marker level codes
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
predict.bqtl
fitted values from QTL models
make.marker.numeric
Translate a marker.frame.object to numeric matrix
plot.map.frame
plots by chromosome location
marker.fill
Map Positions Between Markers
make.analysis.obj
Set up data for QTL mapping
summary.bqtl
Summarize bqtl object
summary.adj
Summarize Laplace approximations
swapf2
Sample F2 loci via approximate posterior
twohk
One and Two Gene Models Using Linearized Posterior
swap
MCMC sampling of multigene models
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
make.state.matrix
Create state.matrix.object
residuals.bqtl
Residuals from QTL models
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
summary.swap
Summarize Gibbs samples for a k-gene model
summary.map.frame
Summary methods for basic data objects
bqtl.fitter
Get loglikelihoods for many models of a common form
twohkbc1
One and Two Gene Models Using Linearized Posterior
varcov
Create moment matrices
map.location
Report map location
map.names
Look up names of markers or loci
A Starting Point
Some Introductory Comments
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
coef.bqtl
Extract Coefficients from fitted objects
bqtl
Bayesian QTL Model Fitting
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
bqtl-internal
Internal BQTL functions
covar
Treat locus as covariate
little.map.dx
Marker Map Description for Simulated Data
little.f2.pheno
Simulated Phenotype Data
little.f2.markers
Simulated Marker Data
formula.bqtl
Extract formula from bqtl object
little.bc.markers
Simulated Marker Data
lapadj
Approximate marginal posterior for chosen model
little.bc.pheno
Simulated Phenotype Data
configs
Lookup loci or effects for genetic model formulas