Function reference • kalis

All functions

Backward(): Propagate a backward table

CacheHaplotypes(): Load haplotypes into optimised package cache

CacheSummary() N() L(): Retrieve information about the haplotype cache

CalcRho(): Calculate recombination probabilities

ClearHaplotypeCache(): Remove all cached haplotypes and free memory

CopyTable(): Copy Forward/Backward tables

DistMat(): Distance matrix

Forward(): Propagate a forward table

MakeBackwardTable(): Create a kalisBackwardTable

MakeForwardTable(): Create a kalisForwardTable

Parameters(): Define a set of Li and Stephens parameters

PostProbs(): Posterior marginal probabilities

QueryCache(): Retrieve haplotypes from memory cache

ResetTable(): Reset Forward/Backward tables

SmallHaps SmallMap: Small example phased haplotype dataset and recombination map

WriteHaplotypes() ReadHaplotypes(): I/O for haplotype matrices in HDF5 files

plot(<kalisDistanceMatrix>): Plotting function for a kalisDistanceMatrix object