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

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

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

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