QTL Bayesian Interval Mapping


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Documentation for package ‘qtlbim’ version 1.9.3

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A B C F P Q S V

-- A --

anova.step.fitqtl Stepwise backward elimination and anova comparison.

-- B --

Bnapus Cross structure for complete Brassica napus data

-- C --

covar.mean Internal qtlbim routines

-- F --

fisch Eight QTL Stephens and Fisch simulated data

-- P --

plot.qb Diagnostics plots for Bayesian interval mapping
plot.qb.BayesFactor Bayesian model selection via Bayes factors.
plot.qb.BestPattern Proximity of common genetic architecture patterns.
plot.qb.close Measures closeness of genetic architectures to target.
plot.qb.confound Examine confounding of covariate with pseudomarkers.
plot.qb.covar Examine GxE effect of covariates on main genetic effects.
plot.qb.diag Marginal and model-conditional summaries of Bayesian interval mapping diagnostics
plot.qb.epistasis Density Plots for Models Showing Epistasis and GxE Interactions.
plot.qb.hpdone Highest probability density (HPD) region.
plot.qb.loci Jittered plot of Bayesian QTL loci samples by chromosome
plot.qb.mainmodes Summaries of QTL modes by chromosome.
plot.qb.meancomp Examine grand mean and covariate MCMC samples.
plot.qb.multloci Summaries of multiple loci on a chromosome.
plot.qb.pairloci Summaries of epistatic pairs of loci.
plot.qb.scanone Plot or print qb.scanone object.
plot.qb.scantwo Two dimensional LOD Plot of Epistasis/joint
plot.qb.sliceone Genome Slice to detect QTL for Phenotypic Trait
plot.qb.slicetwo Slices for epistatic pairs.
plot.qb.varcomp Variance components for Bayesian multiple QTL
print.qb Diagnostics plots for Bayesian interval mapping
print.qb.arch Build genetic architecture with chromosomes, positions and epistatic pairs.
print.qb.BayesFactor Bayesian model selection via Bayes factors.
print.qb.confound Examine confounding of covariate with pseudomarkers.
print.qb.covar Examine GxE effect of covariates on main genetic effects.
print.qb.diag Marginal and model-conditional summaries of Bayesian interval mapping diagnostics
print.qb.epistasis Density Plots for Models Showing Epistasis and GxE Interactions.
print.qb.hpdone Highest probability density (HPD) region.
print.qb.loci Jittered plot of Bayesian QTL loci samples by chromosome
print.qb.meancomp Examine grand mean and covariate MCMC samples.
print.qb.pairloci Summaries of epistatic pairs of loci.
print.qb.scanone Plot or print qb.scanone object.
print.qb.sliceone Genome Slice to detect QTL for Phenotypic Trait
print.qb.slicetwo Slices for epistatic pairs.
print.qb.varcomp Variance components for Bayesian multiple QTL
print.summary.qb.scanone Plot or print qb.scanone object.
print.summary.qb.scantwo Summary of qb.scanone or qb.scantwo object.
pull.grid Internal qtlbim routines
pull.loci Internal qtlbim routines

-- Q --

qb.arch Build genetic architecture with chromosomes, positions and epistatic pairs.
qb.arch.qb.BestPattern Build genetic architecture with chromosomes, positions and epistatic pairs.
qb.arch.step.fitqtl Build genetic architecture with chromosomes, positions and epistatic pairs.
qb.BayesFactor Bayesian model selection via Bayes factors.
qb.best Proximity of common genetic architecture patterns.
qb.BestPattern Proximity of common genetic architecture patterns.
qb.bf Bayesian model selection via Bayes factors.
qb.close Measures closeness of genetic architectures to target.
qb.coda Coerce to an MCMC object for use with the coda package.
qb.confound Examine confounding of covariate with pseudomarkers.
qb.covar Examine GxE effect of covariates on main genetic effects.
qb.cross Internal qtlbim routines
qb.data Prepares data for qb.mcmc
qb.demo Internal qtlbim routines
qb.diag Marginal and model-conditional summaries of Bayesian interval mapping diagnostics
qb.epimodes Summaries of QTL modes by chromosome.
qb.epistasis Density Plots for Models Showing Epistasis and GxE Interactions.
qb.genoprob Grid point and genotype probability computation method
qb.get Internal qtlbim routines
qb.hpdchr Find highest probability density (HPD) region by Chromosome.
qb.hpdone Highest probability density (HPD) region.
qb.intcov Density Plots for Models Showing Epistasis and GxE Interactions.
qb.legacy Legacy update, remove or recover of qb object and associated MCMC samples
qb.load Internal qtlbim routines
qb.loci Jittered plot of Bayesian QTL loci samples by chromosome
qb.mainmodes Summaries of QTL modes by chromosome.
qb.mcmc Bayesian Mutiple Interacting QTL mapping using MCMC
qb.meancomp Examine grand mean and covariate MCMC samples.
qb.model Set up interacting QTL model for qb.mcmc
qb.multloci Summaries of multiple loci on a chromosome.
qb.pairloci Summaries of epistatic pairs of loci.
qb.recover Legacy update, remove or recover of qb object and associated MCMC samples
qb.remove Legacy update, remove or recover of qb object and associated MCMC samples
qb.reorder Internal qtlbim routines
qb.save Internal qtlbim routines
qb.scanone Genome Scan for Main Loci Involved in Phenotypic Trait
qb.scantwo Genome Scan for Pairs of Loci Involved in Phenotypic Trait
qb.sim.cross Simulates QTL related data for an F2 or BC cross.
qb.sliceone Genome Slice to detect QTL for Phenotypic Trait
qb.slicetwo Slices for epistatic pairs.
qb.split.chr Summaries of QTL modes by chromosome.
qb.sweave Run sweave to automate QTL search with MCMC samples.
qb.varcomp Variance components for Bayesian multiple QTL
qbExample MCMC sample for fake BC example
qbHyper MCMC samples for hyper dataset from R/qtl
qbSim MCMC samples used in scan.pdf document
qbSimEpi MCMC samples used in scan.pdf document
qbSimMain MCMC samples used in scan.pdf document

-- S --

sim.data Simulates QTL related data for an F2 or BC cross.
step.fitqtl Stepwise backward elimination and anova comparison.
subset.qb Subsetting Bayesian interval mapping data
summary.qb Diagnostics plots for Bayesian interval mapping
summary.qb.arch Build genetic architecture with chromosomes, positions and epistatic pairs.
summary.qb.BayesFactor Bayesian model selection via Bayes factors.
summary.qb.BestPattern Proximity of common genetic architecture patterns.
summary.qb.close Measures closeness of genetic architectures to target.
summary.qb.confound Examine confounding of covariate with pseudomarkers.
summary.qb.covar Examine GxE effect of covariates on main genetic effects.
summary.qb.diag Marginal and model-conditional summaries of Bayesian interval mapping diagnostics
summary.qb.epistasis Density Plots for Models Showing Epistasis and GxE Interactions.
summary.qb.hpdone Highest probability density (HPD) region.
summary.qb.loci Jittered plot of Bayesian QTL loci samples by chromosome
summary.qb.mainmodes Summaries of QTL modes by chromosome.
summary.qb.meancomp Examine grand mean and covariate MCMC samples.
summary.qb.multloci Summaries of multiple loci on a chromosome.
summary.qb.pairloci Summaries of epistatic pairs of loci.
summary.qb.scanone Summary of qb.scanone or qb.scantwo object.
summary.qb.scantwo Summary of qb.scanone or qb.scantwo object.
summary.qb.sim Simulates QTL related data for an F2 or BC cross.
summary.qb.sliceone Genome Slice to detect QTL for Phenotypic Trait
summary.qb.slicetwo Slices for epistatic pairs.
summary.qb.varcomp Variance components for Bayesian multiple QTL

-- V --

vern Eight week vernalization data for Brassica napus