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bqtl (version 1.0-36)
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
853
Version
1.0-36
License
GPL (>= 2)
Maintainer
Charles C Berry
Last Published
January 29th, 2024
Functions in bqtl (1.0-36)
Search functions
little.f2.pheno
Simulated Phenotype Data
lapadj
Approximate marginal posterior for chosen model
little.bc.markers
Simulated Marker Data
configs
Lookup loci or effects for genetic model formulas
A Starting Point
Some Introductory Comments
little.mf.5
Package of Simulated Marker Map Information
little.ana.bc
A simulated dataset
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
little.map.frame
Package of Simulated Marker Map Information
little.map.dx
Marker Map Description for Simulated Data
bqtl
Bayesian QTL Model Fitting
little.f2.markers
Simulated Marker Data
locus
Lookup loci or effects for genetic model formulas
little.ana.f2
A simulated dataset
little.bc.pheno
Simulated Phenotype Data
bqtl-internal
Internal BQTL functions
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
make.location.prior
Provide a default prior
make.loc.right
Keep track of fully informative markers or states
make.analysis.obj
Set up data for QTL mapping
make.map.frame
Create marker map specifications
make.varcov
Create moment matrices
map.index
Look up numerical index(es) of map locations
make.marker.numeric
Translate a marker.frame.object to numeric matrix
marker.levels
Define marker level codes
make.regressor.matrix
Create regressors using expected marker values
plot.map.frame
plots by chromosome location
marker.fill
Map Positions Between Markers
residuals.bqtl
Residuals from QTL models
summary.adj
Summarize Laplace approximations
map.names
Look up names of markers or loci
make.state.matrix
Create state.matrix.object
summary.bqtl
Summarize bqtl object
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
predict.bqtl
fitted values from QTL models
summary.map.frame
Summary methods for basic data objects
map.location
Report map location
swap
MCMC sampling of multigene models
bqtl.fitter
Get loglikelihoods for many models of a common form
twohkbc1
One and Two Gene Models Using Linearized Posterior
summary.swap
Summarize Gibbs samples for a k-gene model
varcov
Create moment matrices
twohk
One and Two Gene Models Using Linearized Posterior
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
swapf2
Sample F2 loci via approximate posterior
formula.bqtl
Extract formula from bqtl object
coef.bqtl
Extract Coefficients from fitted objects
covar
Treat locus as covariate