bqtl: Bayesian QTL Mapping Toolkit

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
http://famprevmed.ucsd.edu/faculty/cberry/bqtl/

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

Functions

add Man page
adjust.linear.bayes Man page
bc1.levels Man page
bqtl Man page
bqtl.fitter Man page
bqtl-package Man page
coef.bqtl Man page
coef.bqtl.list Man page
configs Man page
covar Man page
dom Man page
\%equiv\% Man page
f2.levels Man page
fitted.bqtl Man page
fitted.linear.bayes Man page
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
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.location.prior Man page
make.loc.right 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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.