bqtl: Bayesian QTL Mapping Toolkit
Version 1.0-32

QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools.

AuthorCharles C. Berry <cberry@ucsd.edu>
Date of publication2016-01-29 00:36:21
MaintainerCharles C. Berry <cberry@ucsd.edu>
LicenseGPL (>= 2)
Version1.0-32
URL http://famprevmed.ucsd.edu/faculty/cberry/bqtl/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bqtl")

Popular man pages

coef.bqtl: Extract Coefficients from fitted objects
little.bc.markers: Simulated Marker Data
little.dx: Marker Map Description for Simulated Data
make.state.matrix: Create state.matrix.object
predict.linear.bayes: Residuals or Predicted Values for linear.bayes objects
residuals.bqtl: Residuals from QTL models
swapbc1: Sample BC1 or Recombinant Inbred loci via approximate...
See all...

All man pages Function index File listing

Man pages

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

Functions

\%equiv\% Man page
add Man page
adjust.linear.bayes Man page
bc1.levels Man page
bqtl Man page
bqtl-package Man page
bqtl.fitter Man page
coef.bqtl Man page
coef.bqtl.list Man page
configs Man page Source code
covar Man page
dom Man page
f2.levels Man page
fitted.bqtl Man page
fitted.linear.bayes Man page
formals Source code
formula.bqtl Man page
lapadj Man page
linear.bayes Man page
little.ana.bc Man page
little.ana.f2 Man page
little.bc.markers Man page
little.bc.pheno Man page
little.f2.markers Man page
little.f2.pheno Man page
little.map.dx Man page
little.map.frame Man page
little.mf.5 Man page
locus Man page Source code
loglik Man page
loglik.bqtl Man page
loglik.bqtl.list Man page
loglik.default Man page
logpost Man page
logpost.bqtl Man page
logpost.bqtl.list Man page
logpost.default Man page
make.analysis.obj Man page
make.loc.right Man page
make.location.prior Man page
make.map.frame Man page
make.marker.numeric Man page
make.regressor.matrix Man page
make.state.matrix Man page
make.varcov Man page
map.dx Man page
map.index Man page
map.index.analysis.object Man page
map.index.default Man page
map.loc Man page
map.location Man page
map.location.analysis.object Man page
map.location.bqtl Man page
map.location.bqtl.list Man page
map.location.default Man page
map.names Man page
map.names.analysis.object Man page
map.names.bqtl Man page
map.names.bqtl.list Man page
map.names.default Man page
map.names.map.frame Man page
marker.fill Man page
marker.levels Man page
plot.analysis.object Man page
plot.map.frame Man page
posterior Man page
posterior.bqtl Man page
posterior.bqtl.list Man page
posterior.default Man page
predict.bqtl Man page
predict.linear.bayes Man page
residuals.bqtl Man page
residuals.linear.bayes Man page
rhs.bqtl Man page
ri.levels Man page
summary.adj Man page
summary.analysis.object Man page
summary.bqtl Man page
summary.map.frame Man page
summary.swap Man page
swap Man page
swapbc1 Man page
swapf2 Man page
twohk Man page
twohkbc1 Man page
twohkf2 Man page
uniq.config Man page
varcov Man page
version.bqtl Man page
zero.dup Man page

Files

src
src/Makevars
src/condreg.c
src/upbqtl.c
src/conCk.c
src/llkEm.c
src/hkreg.c
src/twohkbc1.c
src/lapadj.h
src/swapbc1.c
src/swapf2.c
src/f2wt2.c
src/lapadj.c
src/bc1wt.c
src/lapWHL.c
src/hessup.f
src/normLogLik.c
src/twohkf2.c
NAMESPACE
data
data/little.mf.5.RData
data/little.map.frame.RData
data/little.bc.pheno.tab.gz
data/little.ana.bc.RData
data/little.f2.markers.tab.gz
data/little.f2.pheno.tab.gz
data/little.map.dx.tab.gz
data/little.ana.f2.RData
data/little.bc.markers.tab.gz
R
R/make.loc.right.s
R/residuals.bqtl.s
R/make.marker.numeric.s
R/summary.map.frame.s
R/predict.bqtl.s
R/swapbc1.c.s
R/adjust.linear.bayes.s
R/twohkf2.s
R/zero.dup.s
R/make.location.prior.s
R/map.dx.s
R/rhs.bqtl.s
R/dom.s
R/summary.analysis.object.s
R/make.regressor.matrix.s
R/plot.map.frame.s
R/marker.fill.s
R/version.bqtl.R
R/marker.levels.s
R/locus.s
R/twohkbc1.s
R/map.index.s
R/summary.swap.s
R/plot.analysis.object.s
R/summary.adj.s
R/unique.config.s
R/swapf2.c.s
R/bqtl.s
R/make.state.matrix.s
R/twohk.s
R/equiv.s
R/add.s
R/make.analysis.obj.s
R/map.methods.s
R/update.bqtl.s
R/formula.methods.s
R/methods.s
R/lapadj.s
R/make.varcov.s
R/configs.s
R/make.map.frame.s
R/varcov.s
R/covar.s
R/predict.linear.bayes.s
R/is.element.s
R/swap.s
R/linear.bayes.s
MD5
DESCRIPTION
man
man/marker.fill.Rd
man/summary.adj.Rd
man/map.names.Rd
man/little.ana.f2.Rd
man/adjust.linear.bayes.Rd
man/make.state.matrix.Rd
man/varcov.Rd
man/swap.Rd
man/swapbc1.Rd
man/swapf2.Rd
man/summary.swap.Rd
man/make.varcov.Rd
man/little.mf.5.Rd
man/summary.map.frame.Rd
man/make.marker.numeric.Rd
man/little.dx.Rd
man/map.index.Rd
man/twohkbc1.Rd
man/linear.bayes.Rd
man/covar.Rd
man/plot.map.frame.Rd
man/make.map.frame.Rd
man/little.bc.pheno.Rd
man/bqtl-internal.Rd
man/make.location.prior.Rd
man/a.starting.point.for.bqtl.Rd
man/map.location.Rd
man/loglik.Rd
man/coef.bqtl.Rd
man/predict.bqtl.Rd
man/make.analysis.obj.Rd
man/little.bc.markers.Rd
man/make.loc.right.Rd
man/little.f2.pheno.Rd
man/residuals.bqtl.Rd
man/twohk.Rd
man/bqtl.Rd
man/formula.bqtl.Rd
man/little.f2.markers.Rd
man/predict.linear.bayes.Rd
man/little.ana.bc.Rd
man/summary.bqtl.Rd
man/marker.levels.Rd
man/locus.Rd
man/make.regressor.matrix.Rd
man/configs.Rd
man/little.map.frame.Rd
man/update.bqtl.Rd
man/lapadj.Rd
INDEX
CHANGES
bqtl documentation built on May 19, 2017, 11:42 p.m.

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