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bqtl (version 1.0-38)
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
1.0-38
License
GPL (>= 2)
Maintainer
Charles C Berry
Last Published
September 24th, 2024
Functions in bqtl (1.0-38)
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little.bc.markers
Simulated Marker Data
map.index
Look up numerical index(es) of map locations
make.varcov
Create moment matrices
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
make.analysis.obj
Set up data for QTL mapping
make.state.matrix
Create state.matrix.object
summary.adj
Summarize Laplace approximations
make.regressor.matrix
Create regressors using expected marker values
summary.bqtl
Summarize bqtl object
marker.levels
Define marker level codes
summary.map.frame
Summary methods for basic data objects
map.names
Look up names of markers or loci
marker.fill
Map Positions Between Markers
summary.swap
Summarize Gibbs samples for a k-gene model
bqtl.fitter
Get loglikelihoods for many models of a common form
map.location
Report map location
twohkbc1
One and Two Gene Models Using Linearized Posterior
swap
MCMC sampling of multigene models
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
little.bc.pheno
Simulated Phenotype Data
make.loc.right
Keep track of fully informative markers or states
twohk
One and Two Gene Models Using Linearized Posterior
predict.bqtl
fitted values from QTL models
plot.map.frame
plots by chromosome location
swapf2
Sample F2 loci via approximate posterior
make.location.prior
Provide a default prior
varcov
Create moment matrices
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
residuals.bqtl
Residuals from QTL models
make.map.frame
Create marker map specifications
make.marker.numeric
Translate a marker.frame.object to numeric matrix
bqtl-internal
Internal BQTL functions
little.map.dx
Marker Map Description for Simulated Data
configs
Lookup loci or effects for genetic model formulas
little.mf.5
Package of Simulated Marker Map Information
formula.bqtl
Extract formula from bqtl object
little.map.frame
Package of Simulated Marker Map Information
A Starting Point
Some Introductory Comments
covar
Treat locus as covariate
little.ana.bc
A simulated dataset
lapadj
Approximate marginal posterior for chosen model
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
bqtl
Bayesian QTL Model Fitting
little.f2.pheno
Simulated Phenotype Data
coef.bqtl
Extract Coefficients from fitted objects
locus
Lookup loci or effects for genetic model formulas
little.f2.markers
Simulated Marker Data
little.ana.f2
A simulated dataset