R: Bayesian QTL Mapping Toolkit

# Bayesian QTL Mapping Toolkit

## Documentation for package ‘bqtl’ version 1.0-39

- DESCRIPTION file

## Help Pages

bqtl-package | Some Introductory Comments
%equiv% | Internal BQTL functions
add | Lookup loci or effects for genetic model formulas
adjust.linear.bayes | Use Laplace Approximations to improve linear approximations to the posterior
bc1.levels | Define marker level codes
bqtl | Bayesian QTL Model Fitting
bqtl.fitter | Get loglikelihoods for many models of a common form
coef.bqtl | Extract Coefficients from fitted objects
coef.bqtl.list | Extract Coefficients from fitted objects
configs | Lookup loci or effects for genetic model formulas
covar | Treat locus as covariate
dom | Lookup loci or effects for genetic model formulas
f2.levels | Define marker level codes
fitted.bqtl | fitted values from QTL models
fitted.linear.bayes | Residuals or Predicted Values for linear.bayes objects
formula.bqtl | Extract formula from bqtl object
lapadj | Approximate marginal posterior for chosen model
linear.bayes | Bayesian QTL mapping via Linearized Likelihood
little.ana.bc | A simulated dataset
little.ana.f2 | A simulated dataset
little.bc.markers | Simulated Marker Data
little.bc.pheno | Simulated Phenotype Data
little.f2.markers | Simulated Marker Data
little.f2.pheno | Simulated Phenotype Data
little.map.dx | Marker Map Description for Simulated Data
little.map.frame | Package of Simulated Marker Map Information
little.mf.5 | Package of Simulated Marker Map Information
locus | Lookup loci or effects for genetic model formulas
loglik | Extract loglikelihood, log posterior, or posterior from fitted models
loglik.bqtl | Extract loglikelihood, log posterior, or posterior from fitted models
loglik.bqtl.list | Extract loglikelihood, log posterior, or posterior from fitted models
loglik.default | Extract loglikelihood, log posterior, or posterior from fitted models
logpost | Extract loglikelihood, log posterior, or posterior from fitted models
logpost.bqtl | Extract loglikelihood, log posterior, or posterior from fitted models
logpost.bqtl.list | Extract loglikelihood, log posterior, or posterior from fitted models
logpost.default | Extract loglikelihood, log posterior, or posterior from fitted models
make.analysis.obj | Set up data for QTL mapping
make.loc.right | Keep track of fully informative markers or states
make.location.prior | Provide a default prior
make.map.frame | Create marker map specifications
make.marker.numeric | Translate a marker.frame.object to numeric matrix
make.regressor.matrix | Create regressors using expected marker values
make.state.matrix | Create state.matrix.object
make.varcov | Create moment matrices
map.dx | Internal BQTL functions
map.index | Look up numerical index(es) of map locations
map.index.analysis.object | Look up numerical index(es) of map locations
map.index.default | Look up numerical index(es) of map locations
map.loc | Report map location
map.location | Report map location
map.location.analysis.object | Report map location
map.location.bqtl | Report map location
map.location.bqtl.list | Report map location
map.location.default | Report map location
map.names | Look up names of markers or loci
map.names.analysis.object | Look up names of markers or loci
map.names.bqtl | Look up names of markers or loci
map.names.bqtl.list | Look up names of markers or loci
map.names.default | Look up names of markers or loci
map.names.map.frame | Look up names of markers or loci
marker.fill | Map Positions Between Markers
marker.levels | Define marker level codes
plot.analysis.object | plots by chromosome location
plot.map.frame | plots by chromosome location
posterior | Extract loglikelihood, log posterior, or posterior from fitted models
posterior.bqtl | Extract loglikelihood, log posterior, or posterior from fitted models
posterior.bqtl.list | Extract loglikelihood, log posterior, or posterior from fitted models
posterior.default | Extract loglikelihood, log posterior, or posterior from fitted models
predict.bqtl | fitted values from QTL models
predict.linear.bayes | Residuals or Predicted Values for linear.bayes objects
residuals.bqtl | Residuals from QTL models
residuals.linear.bayes | Residuals or Predicted Values for linear.bayes objects
rhs.bqtl | Internal BQTL functions
ri.levels | Define marker level codes
summary.adj | Summarize Laplace approximations
summary.analysis.object | Summary methods for basic data objects
summary.bqtl | Summarize bqtl object
summary.map.frame | Summary methods for basic data objects
summary.swap | Summarize Gibbs samples for a k-gene model
swap | MCMC sampling of multigene models
swapbc1 | Sample BC1 or Recombinant Inbred loci via approximate posterior.
swapf2 | Sample F2 loci via approximate posterior
twohk | One and Two Gene Models Using Linearized Posterior
twohkbc1 | One and Two Gene Models Using Linearized Posterior
twohkf2 | One and Two Gene Models Using Linearized Posterior
uniq.config | Internal BQTL functions
varcov | Create moment matrices
version.bqtl | Internal BQTL functions
zero.dup | Internal BQTL functions