QTL Bayesian Interval Mapping


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Documentation for package `qtlbim' version 1.6.0

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anova.step.fitqtl Stepwise backward elimination and anova comparison.
Bnapus Cross structure for complete Brassica napus data
fisch Eight QTL Stephens and Fisch simulated data
plot.qb Diagnostics plots for Bayesian interval mapping
plot.qb.BayesFactor Bayesian model selection via Bayes factors.
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
plot.qb.hpdone Highest probability density (HPD) region.
plot.qb.loci Jittered plot of Bayesian QTL loci samples 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.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
print.qb.hpdone Highest probability density (HPD) region.
print.qb.meancomp Examine grand mean and covariate MCMC samples.
print.qb.multloci Summaries of multiple loci on a chromosome.
print.qb.pairloci Summaries of epistatic pairs of loci.
print.qb.scanone Plot or print qb.scanone object.
print.qb.scantwo Two dimensional LOD Plot of Epistasis/joint
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
pull.grid Internal qtlbim routines
qb.arch 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.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.epistasis Density Plots for Models Showing Epistasis
qb.genoprob Grid point and genotype probability computation method
qb.get Internal qtlbim routines
qb.hpdone Highest probability density (HPD) region.
qb.load Internal qtlbim routines
qb.loci Jittered plot of Bayesian QTL loci samples 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 Remove or recover qb object and associated MCMC samples
qb.remove Remove or recover 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.sweave Run sweave to automate QTL search with MCMC samples.
qb.varcomp Variance components for Bayesian multiple QTL
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.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
summary.qb.hpdone Highest probability density (HPD) region.
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
vern Eight week vernalization data for Brassica napus