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| anova.step.fitqtl | Stepwise backward elimination and anova comparison. |
| Bnapus | Cross structure for complete Brassica napus data |
| covar.mean | Internal qtlbim routines |
| 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.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 |
| qb.arch | Build genetic architecture with chromosomes, positions and epistatic pairs. |
| qb.arch.default | 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.cross.class | 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 |
| 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 |
| vern | Eight week vernalization data for Brassica napus |