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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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Version

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)

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