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| %equiv% | Internal BQTL functions |
| A Starting Point | Some Introductory Comments |
| 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 |
| 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.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.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.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.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.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 |