Package index
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Backward()
- Propagate a backward table
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CacheHaplotypes()
- Load haplotypes into optimised package cache
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CacheSummary()
N()
L()
- Retrieve information about the haplotype cache
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CalcRho()
- Calculate recombination probabilities
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ClearHaplotypeCache()
- Remove all cached haplotypes and free memory
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CopyTable()
- Copy Forward/Backward tables
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DistMat()
- Distance matrix
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Forward()
- Propagate a forward table
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MakeBackwardTable()
- Create a
kalisBackwardTable
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MakeForwardTable()
- Create a
kalisForwardTable
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Parameters()
- Define a set of Li and Stephens parameters
-
PostProbs()
- Posterior marginal probabilities
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QueryCache()
- Retrieve haplotypes from memory cache
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ResetTable()
- Reset Forward/Backward tables
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WriteHaplotypes()
ReadHaplotypes()
- I/O for haplotype matrices in HDF5 files
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plot(<kalisDistanceMatrix>)
- Plotting function for a kalisDistanceMatrix object