Entry: Happy
Aliases: introduction happy happy.matrices happy.save
Keywords: models
Description: Quantitative Trait Locus analysis in Heterogeneous Stocks
URL: ../../../library/happy/html/AAA-happy.html

Entry: epistasis
Aliases: epistasis epistasispair
Keywords: models
Description: Analysis of Epistasis between Markers
URL: ../../../library/happy/html/epistasis.html

Entry: gfit
Aliases: gaussian.iterate gaussian.null gaussian.loop gaussian.init gaussian.fn gaussian.gr gfit
Keywords: models
Description: Fit a Gaussian Mixture Model to an object returned by happy()
URL: ../../../library/happy/html/gauss.html

Entry: happy-internal
Aliases: happy-internal comparelist matrixSquared mfit twofit condfit strain.effects glmfit sdp hprob2 hnonrecomb h.sum.prob2
Keywords: internal
Description: Internal Happy Functions
URL: ../../../library/happy/html/happy-internal.html

Entry: happyplot
Aliases: happyplot mergeplot
Keywords: aplot
Description: Plotting functions for happy model fits
URL: ../../../library/happy/html/happyplot.html

Entry: cache
Aliases: save.genome save.happy load.genome load.markers the.chromosomes
Keywords: models
Description: Save HAPPY design matrices and genotypes to disk for rapid reloading
URL: ../../../library/happy/html/hcache.html

Entry: hdesign
Aliases: hdesign hprob hgenotype
Keywords: models
Description: Extract design matrix or genotypes for a specific marker interval from a happy object
URL: ../../../library/happy/html/hdesign.html

Entry: hfit
Aliases: hfit hfit.sequential pfit normalise
Keywords: models
Description: Fit a model to an object returned by happy()
URL: ../../../library/happy/html/hfit.html

Entry: mergelist
Aliases: mergelist
Keywords: models
Description: Create an object descrbing how to merge strains together
URL: ../../../library/happy/html/mergelist.html

Entry: mergematrices
Aliases: mergedpositionmatrix mergematrices
Keywords: models
Description: Construct matrices used to merge together founder strains
URL: ../../../library/happy/html/mergematrices.html

Entry: mergeprepare
Aliases: mergeprepare mergefit fastmergefit condmergefit
Keywords: models
Description: Perform tests to determine whether individual polymorphisms could have given rise to a QTL
URL: ../../../library/happy/html/mergeprepare.html
