# Quantitative Trait Locus genetic analysis in Heterogeneous Stocks

## Documentation for package ‘happy.hbrem’ version 2.4

- DESCRIPTION file.

## Help Pages

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