Bayesian QTL Mapping Toolkit


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Documentation for package ‘bqtl’ version 1.0-33

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