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bqtl (version 1.0-5)
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
574
Version
1.0-5
License
GPL version 2 or later
Maintainer
Charles C Berry
Last Published
September 24th, 2024
Functions in bqtl (1.0-5)
Search all functions
bqtl
Bayesian QTL Model Fitting
summary.swap
Summarize Gibbs samples for a k-gene model
configs
Lookup loci or effects for genetic model formulas
map.names
Look up names of markers or loci
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
twohk
One and Two Gene Models Using Linearized Posterior
bqtl-internal
Internal BQTL functions
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
map.index
Look up numerical index(es) of map locations
little.ana.bc
A simulated dataset
formula.bqtl
Extract formula from bqtl object
marker.fill
Map Positions Between Markers
make.state.matrix
Create state.matrix.object
lapadj
Approximate marginal posterior for chosen model
make.map.frame
Create marker map specifications
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
swap
MCMC sampling of multigene models
make.marker.numeric
Translate a marker.frame.object to numeric matrix
bqtl.fitter
Get loglikelihoods for many models of a common form
marker.levels
Define marker level codes
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
A Starting Point
Some Introductory Comments
varcov
Create moment matrices
swapf2
Sample F2 loci via approximate posterior
make.location.prior
Provide a default prior
summary.adj
Summarize Laplace approximations
summary.map.frame
Summary methods for basic data objects
predict.bqtl
fitted values from QTL models
coef.bqtl
Extract Coefficients from fitted objects
residuals.bqtl
Residuals from QTL models
locus
Lookup loci or effects for genetic model formulas
plot.map.frame
plots by chromosome location
make.varcov
Create moment matrices
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
map.location
Report map location
covar
Treat locus as covariate
twohkbc1
One and Two Gene Models Using Linearized Posterior
summary.bqtl
Summarize bqtl object
make.regressor.matrix
Create regressors using expected marker values
make.analysis.obj
Set up data for QTL mapping
make.loc.right
Keep track of fully informative markers or states
little.f2.markers
Simulated Marker Data
little.mf.5
Package of Simulated Marker Map Information
little.map.frame
Package of Simulated Marker Map Information
little.bc.pheno
Simulated Phenotype Data
little.bc.markers
Simulated Marker Data
little.f2.pheno
Simulated Phenotype Data
little.ana.f2
A simulated dataset
little.dx
Marker Map Description for Simulated Data