Entry: A Starting Point
Aliases: A Starting Point
Keywords: regression
Description: Some Introductory Comments
URL: ../../../library/bqtl/html/a.starting.point.for.bqtl.html

Entry: adjust.linear.bayes
Aliases: adjust.linear.bayes
Keywords: regression
Description: Use Laplace Approximations to improve linear approximations to the posterior
URL: ../../../library/bqtl/html/adjust.linear.bayes.html

Entry: bqtl-internal
Aliases: %equiv% map.dx rhs.bqtl uniq.config zero.dup version.bqtl
Keywords: utilities
Description: Internal BQTL functions
URL: ../../../library/bqtl/html/bqtl-internal.html

Entry: bqtl
Aliases: bqtl
Keywords: regression
Description: Bayesian QTL Model Fitting
URL: ../../../library/bqtl/html/bqtl.html

Entry: coef.bqtl
Aliases: coef.bqtl coef.bqtl.list
Keywords: methods
Description: Extract Coefficients from fitted objects
URL: ../../../library/bqtl/html/coef.bqtl.html

Entry: configs
Aliases: configs
Keywords: utilities
Description: Lookup loci or effects for genetic model formulas
URL: ../../../library/bqtl/html/configs.html

Entry: covar
Aliases: covar
Keywords: regression
Description: Treat locus as covariate
URL: ../../../library/bqtl/html/covar.html

Entry: formula.bqtl
Aliases: formula.bqtl
Keywords: methods
Description: Extract formula from bqtl object
URL: ../../../library/bqtl/html/formula.bqtl.html

Entry: lapadj
Aliases: lapadj
Keywords: regression
Description: Approximate marginal posterior for chosen model
URL: ../../../library/bqtl/html/lapadj.html

Entry: linear.bayes
Aliases: linear.bayes
Keywords: regression
Description: Bayesian QTL mapping via Linearized Likelihood
URL: ../../../library/bqtl/html/linear.bayes.html

Entry: little.ana.bc
Aliases: little.ana.bc
Keywords: datasets
Description: A simulated dataset
URL: ../../../library/bqtl/html/little.ana.bc.html

Entry: little.ana.f2
Aliases: little.ana.f2
Keywords: datasets
Description: A simulated dataset
URL: ../../../library/bqtl/html/little.ana.f2.html

Entry: little.bc.markers
Aliases: little.bc.markers
Keywords: datasets
Description: Simulated Marker Data
URL: ../../../library/bqtl/html/little.bc.markers.html

Entry: little.bc.pheno
Aliases: little.bc.pheno
Keywords: datasets
Description: Simulated Phenotype Data
URL: ../../../library/bqtl/html/little.bc.pheno.html

Entry: little.map.dx
Aliases: little.map.dx
Keywords: datasets
Description: Marker Map Description for Simulated Data
URL: ../../../library/bqtl/html/little.dx.html

Entry: little.f2.markers
Aliases: little.f2.markers
Keywords: datasets
Description: Simulated Marker Data
URL: ../../../library/bqtl/html/little.f2.markers.html

Entry: little.f2.pheno
Aliases: little.f2.pheno
Keywords: datasets
Description: Simulated Phenotype Data
URL: ../../../library/bqtl/html/little.f2.pheno.html

Entry: little.map.frame
Aliases: little.map.frame
Keywords: datasets
Description: Package of Simulated Marker Map Information
URL: ../../../library/bqtl/html/little.map.frame.html

Entry: little.mf.5
Aliases: little.mf.5
Keywords: datasets
Description: Package of Simulated Marker Map Information
URL: ../../../library/bqtl/html/little.mf.5.html

Entry: locus
Aliases: locus add dom
Keywords: regression
Description: Lookup loci or effects for genetic model formulas
URL: ../../../library/bqtl/html/locus.html

Entry: loglik
Aliases: loglik loglik.default loglik.bqtl loglik.bqtl.list logpost logpost.default logpost.bqtl logpost.bqtl.list posterior posterior.default posterior.bqtl posterior.bqtl.list
Keywords: models
Description: Extract loglikelihood, log posterior, or posterior from fitted models
URL: ../../../library/bqtl/html/loglik.html

Entry: make.analysis.obj
Aliases: make.analysis.obj
Keywords: manip
Description: Set up data for QTL mapping
URL: ../../../library/bqtl/html/make.analysis.obj.html

Entry: make.loc.right
Aliases: make.loc.right
Keywords: manip
Description: Keep track of fully informative markers or states
URL: ../../../library/bqtl/html/make.loc.right.html

Entry: make.location.prior
Aliases: make.location.prior
Keywords: utilities
Description: Provide a default prior
URL: ../../../library/bqtl/html/make.location.prior.html

Entry: make.map.frame
Aliases: make.map.frame
Keywords: manip
Description: Create marker map specifications
URL: ../../../library/bqtl/html/make.map.frame.html

Entry: make.marker.numeric
Aliases: make.marker.numeric
Keywords: utilities
Description: Translate a marker.frame.object to numeric matrix
URL: ../../../library/bqtl/html/make.marker.numeric.html

Entry: make.regressor.matrix
Aliases: make.regressor.matrix
Keywords: utilities
Description: Create regressors using expected marker values
URL: ../../../library/bqtl/html/make.regressor.matrix.html

Entry: make.state.matrix
Aliases: make.state.matrix
Keywords: utilities
Description: Create state.matrix.object
URL: ../../../library/bqtl/html/make.state.matrix.html

Entry: make.varcov
Aliases: make.varcov
Keywords: utilities
Description: Create moment matrices
URL: ../../../library/bqtl/html/make.varcov.html

Entry: map.index
Aliases: map.index map.index.default map.index.analysis.object
Keywords: methods
Description: Look up numerical index(es) of map locations
URL: ../../../library/bqtl/html/map.index.html

Entry: map.location
Aliases: map.loc map.location map.location.default map.location.analysis.object map.location.bqtl map.location.bqtl.list
Keywords: regression
Description: Report map location
URL: ../../../library/bqtl/html/map.location.html

Entry: map.names
Aliases: map.names map.names.default map.names.bqtl map.names.bqtl.list map.names.analysis.object map.names.map.frame
Keywords: utilities
Description: Look up names of markers or loci
URL: ../../../library/bqtl/html/map.names.html

Entry: marker.fill
Aliases: marker.fill
Keywords: utilities
Description: Map Positions Between Markers
URL: ../../../library/bqtl/html/marker.fill.html

Entry: marker.levels
Aliases: marker.levels bc1.levels f2.levels ri.levels
Keywords: manip
Description: Define marker level codes
URL: ../../../library/bqtl/html/marker.levels.html

Entry: plot.map.frame
Aliases: plot.map.frame plot.analysis.object
Keywords: hplot
Description: plots by chromosome location
URL: ../../../library/bqtl/html/plot.map.frame.html

Entry: predict.bqtl
Aliases: predict.bqtl fitted.bqtl
Keywords: methods
Description: fitted values from QTL models
URL: ../../../library/bqtl/html/predict.bqtl.html

Entry: predict.linear.bayes
Aliases: predict.linear.bayes fitted.linear.bayes residuals.linear.bayes
Keywords: methods
Description: Residuals or Predicted Values for linear.bayes objects
URL: ../../../library/bqtl/html/predict.linear.bayes.html

Entry: residuals.bqtl
Aliases: residuals.bqtl
Keywords: methods
Description: Residuals from QTL models
URL: ../../../library/bqtl/html/residuals.bqtl.html

Entry: summary.adj
Aliases: summary.adj
Keywords: methods
Description: Summarize Laplace approximations
URL: ../../../library/bqtl/html/summary.adj.html

Entry: summary.bqtl
Aliases: summary.bqtl
Keywords: methods
Description: Summarize bqtl object
URL: ../../../library/bqtl/html/summary.bqtl.html

Entry: summary.map.frame
Aliases: summary.map.frame summary.analysis.object
Keywords: methods
Description: Summary methods for basic data objects
URL: ../../../library/bqtl/html/summary.map.frame.html

Entry: summary.swap
Aliases: summary.swap
Keywords: methods
Description: Summarize Gibbs samples for a k-gene model
URL: ../../../library/bqtl/html/summary.swap.html

Entry: swap
Aliases: swap
Keywords: regression
Description: MCMC sampling of multigene models
URL: ../../../library/bqtl/html/swap.html

Entry: swapbc1
Aliases: swapbc1
Keywords: utilities
Description: Sample BC1 or Recombinant Inbred loci via approximate posterior.
URL: ../../../library/bqtl/html/swapbc1.html

Entry: swapf2
Aliases: swapf2
Keywords: utilities
Description: Sample F2 loci via approximate posterior
URL: ../../../library/bqtl/html/swapf2.html

Entry: twohk
Aliases: twohk
Keywords: models
Description: One and Two Gene Models Using Linearized Posterior
URL: ../../../library/bqtl/html/twohk.html

Entry: twohkbc1
Aliases: twohkbc1 twohkf2
Keywords: utilities
Description: One and Two Gene Models Using Linearized Posterior
URL: ../../../library/bqtl/html/twohkbc1.html

Entry: bqtl.fitter
Aliases: bqtl.fitter
Keywords: models
Description: Get loglikelihoods for many models of a common form
URL: ../../../library/bqtl/html/update.bqtl.html

Entry: varcov
Aliases: varcov
Keywords: utilities
Description: Create moment matrices
URL: ../../../library/bqtl/html/varcov.html
