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| condmergefit | Perform tests to determine whether individual polymorphisms could have given rise to a QTL |
| epistasis | Analysis of Epistasis between Markers |
| epistasispair | Analysis of Epistasis between Markers |
| fastmergefit | Perform tests to determine whether individual polymorphisms could have given rise to a QTL |
| gaussian.fn | Fit a Gaussian Mixture Model to an object returned by happy() |
| gaussian.gr | Fit a Gaussian Mixture Model to an object returned by happy() |
| gaussian.init | Fit a Gaussian Mixture Model to an object returned by happy() |
| gaussian.iterate | Fit a Gaussian Mixture Model to an object returned by happy() |
| gaussian.loop | Fit a Gaussian Mixture Model to an object returned by happy() |
| gaussian.null | Fit a Gaussian Mixture Model to an object returned by happy() |
| gfit | Fit a Gaussian Mixture Model to an object returned by happy() |
| happy | Quantitative Trait Locus analysis in Heterogeneous Stocks |
| happy.matrices | Quantitative Trait Locus analysis in Heterogeneous Stocks |
| happy.save | Quantitative Trait Locus analysis in Heterogeneous Stocks |
| happyplot | Plotting functions for happy model fits |
| hdesign | Extract design matrix or genotypes for a specific marker interval from a happy object |
| hfit | Fit a model to an object returned by happy() |
| hfit.sequential | Fit a model to an object returned by happy() |
| hgenotype | Extract design matrix or genotypes for a specific marker interval from a happy object |
| hprob | Extract design matrix or genotypes for a specific marker interval from a happy object |
| introduction | Quantitative Trait Locus analysis in Heterogeneous Stocks |
| load.genome | Save HAPPY design matrices and genotypes to disk for rapid reloading |
| load.markers | Save HAPPY design matrices and genotypes to disk for rapid reloading |
| mergedpositionmatrix | Construct matrices used to merge together founder strains |
| mergefit | Perform tests to determine whether individual polymorphisms could have given rise to a QTL |
| mergelist | Create an object descrbing how to merge strains together |
| mergematrices | Construct matrices used to merge together founder strains |
| mergeplot | Plotting functions for happy model fits |
| mergeprepare | Perform tests to determine whether individual polymorphisms could have given rise to a QTL |
| normalise | Fit a model to an object returned by happy() |
| pfit | Fit a model to an object returned by happy() |
| save.genome | Save HAPPY design matrices and genotypes to disk for rapid reloading |
| save.happy | Save HAPPY design matrices and genotypes to disk for rapid reloading |
| the.chromosomes | Save HAPPY design matrices and genotypes to disk for rapid reloading |