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bqtl (version 1.0-7)
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
629
Version
1.0-7
License
GPL version 2 or later
Maintainer
Charles C Berry
Last Published
September 24th, 2024
Functions in bqtl (1.0-7)
Search all functions
A Starting Point
Some Introductory Comments
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
configs
Lookup loci or effects for genetic model formulas
bqtl-internal
Internal BQTL functions
formula.bqtl
Extract formula from bqtl object
covar
Treat locus as covariate
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
lapadj
Approximate marginal posterior for chosen model
make.marker.numeric
Translate a marker.frame.object to numeric matrix
make.location.prior
Provide a default prior
bqtl.fitter
Get loglikelihoods for many models of a common form
make.map.frame
Create marker map specifications
residuals.bqtl
Residuals from QTL models
twohk
One and Two Gene Models Using Linearized Posterior
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
marker.levels
Define marker level codes
bqtl
Bayesian QTL Model Fitting
make.varcov
Create moment matrices
locus
Lookup loci or effects for genetic model formulas
plot.map.frame
plots by chromosome location
make.regressor.matrix
Create regressors using expected marker values
varcov
Create moment matrices
summary.swap
Summarize Gibbs samples for a k-gene model
swapf2
Sample F2 loci via approximate posterior
map.index
Look up numerical index(es) of map locations
predict.bqtl
fitted values from QTL models
swap
MCMC sampling of multigene models
map.names
Look up names of markers or loci
coef.bqtl
Extract Coefficients from fitted objects
map.location
Report map location
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
make.state.matrix
Create state.matrix.object
summary.bqtl
Summarize bqtl object
marker.fill
Map Positions Between Markers
little.ana.bc
A simulated dataset
summary.map.frame
Summary methods for basic data objects
twohkbc1
One and Two Gene Models Using Linearized Posterior
make.analysis.obj
Set up data for QTL mapping
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
make.loc.right
Keep track of fully informative markers or states
summary.adj
Summarize Laplace approximations
little.mf.5
Package of Simulated Marker Map Information
little.ana.f2
A simulated dataset
little.map.frame
Package of Simulated Marker Map Information
little.f2.markers
Simulated Marker Data
little.bc.markers
Simulated Marker Data
little.f2.pheno
Simulated Phenotype Data
little.dx
Marker Map Description for Simulated Data
little.bc.pheno
Simulated Phenotype Data