bqtl: Bayesian QTL Mapping Toolkit

Share:

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

Author
Charles C. Berry <cberry@ucsd.edu>
Date of publication
2016-01-29 00:36:21
Maintainer
Charles C. Berry <cberry@ucsd.edu>
License
GPL (>= 2)
Version
1.0-32
URLs

View on CRAN

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

Files in this package

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