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bqtl (version 1.0-29)
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
1.0-29
License
GPL (>= 2)
Maintainer
Charles C Berry
Last Published
May 1st, 2013
Functions in bqtl (1.0-29)
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formula.bqtl
Extract formula from bqtl object
A Starting Point
Some Introductory Comments
linear.bayes
Bayesian QTL mapping via Linearized Likelihood
adjust.linear.bayes
Use Laplace Approximations to improve linear approximations to the posterior
make.map.frame
Create marker map specifications
swap
MCMC sampling of multigene models
map.index
Look up numerical index(es) of map locations
map.names
Look up names of markers or loci
configs
Lookup loci or effects for genetic model formulas
bqtl
Bayesian QTL Model Fitting
make.varcov
Create moment matrices
little.mf.5
Package of Simulated Marker Map Information
bqtl.fitter
Get loglikelihoods for many models of a common form
bqtl-internal
Internal BQTL functions
swapbc1
Sample BC1 or Recombinant Inbred loci via approximate posterior.
little.ana.f2
A simulated dataset
make.state.matrix
Create state.matrix.object
loglik
Extract loglikelihood, log posterior, or posterior from fitted models
map.location
Report map location
little.f2.pheno
Simulated Phenotype Data
little.map.dx
Marker Map Description for Simulated Data
summary.adj
Summarize Laplace approximations
lapadj
Approximate marginal posterior for chosen model
residuals.bqtl
Residuals from QTL models
marker.fill
Map Positions Between Markers
summary.map.frame
Summary methods for basic data objects
make.regressor.matrix
Create regressors using expected marker values
marker.levels
Define marker level codes
make.location.prior
Provide a default prior
twohk
One and Two Gene Models Using Linearized Posterior
summary.bqtl
Summarize bqtl object
covar
Treat locus as covariate
make.analysis.obj
Set up data for QTL mapping
little.f2.markers
Simulated Marker Data
predict.linear.bayes
Residuals or Predicted Values for linear.bayes objects
little.map.frame
Package of Simulated Marker Map Information
plot.map.frame
plots by chromosome location
make.marker.numeric
Translate a marker.frame.object to numeric matrix
swapf2
Sample F2 loci via approximate posterior
coef.bqtl
Extract Coefficients from fitted objects
little.bc.pheno
Simulated Phenotype Data
summary.swap
Summarize Gibbs samples for a k-gene model
varcov
Create moment matrices
twohkbc1
One and Two Gene Models Using Linearized Posterior
little.ana.bc
A simulated dataset
locus
Lookup loci or effects for genetic model formulas
little.bc.markers
Simulated Marker Data
predict.bqtl
fitted values from QTL models
make.loc.right
Keep track of fully informative markers or states