Package index • kalis

All functions

Backward(): Propagate a backward table

CacheHaplotypes(): Load haplotypes into optimised package cache

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

CalcCheckpointTables(): Calculate Checkpoint Tables

CalcRho(): Calculate recombination probabilities

CalcTraces(): Fast Calculation of Matrix Trace and Hilbert Schmidt Norm

CladeMat(): Fast clade matrix construction

ClearHaplotypeCache(): Remove all cached haplotypes and free memory

CopyTable(): Copy Forward/Backward tables

CreateForwardTableCache(): Create cache for forward tables

DistMat(): Distance matrix

FillTableCache(): Fill a forward table cache

Forward(): Propagate a forward table

ForwardIterator(): Build an efficient iterator over loci

ForwardUsingTableCache(): Use a forward table cache to propagate

MakeBackwardTable(): Create a kalisBackwardTable

MakeForwardTable(): Create a kalisForwardTable

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

PostProbs(): Posterior marginal probabilities

PruneCladeMat(): Prune called sprigs or singletons from inferred clade matrix

QueryCache(): Retrieve haplotypes from memory cache

ResetTable(): Reset Forward/Backward tables

SmallHaps SmallMap: Small example phased haplotype dataset and recombination map

Sprigs(): Greedy sprig calling based on nearest neighbourhoods

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

plot(<kalisDistanceMatrix>): Plotting function for a distance matrix