# Distance Based Cell Lineage Reconstruction

## Documentation for package ‘DCLEAR’ version 1.0.13

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

add_deletion | add_deletion
add_dropout | add_dropout
as_igraph | Generic function for as_igraph
as_igraph-method | as_igraph
as_igraph-method | as_igraph
as_lineage_tree | Generic function for as_lineage_tree
as_lineage_tree-method | as_lineage_tree
as_phylo | Generic function for as_phylo
as_phylo-method | as_phylo
DCLEAR | DCLEAR: A package for DCLEAR: Distance based Cell LinEAge Reconstruction
dist_kmer_replacement_inference | Core function of computing kmer replacement distance
dist_replacement | Generic function for dist_replacement
dist_replacement-method | Compute the kmer replacement distance
dist_replacement-method | Compute the kmer replacement distance
dist_weighted_hamming | Generic function for dist_weighted_hamming
dist_weighted_hamming-method | dist_weighted_hamming
downsample | Generic function for downsample
downsample-method | downsample
downsample-method | downsample
get_distance_prior | get_distance_prior
get_leaves | Generic function for get_leaves
get_leaves-method | get_leaves
get_node_names | get_node_names
get_replacement_probability | get_replacement_probability
get_sequence | get_sequence
get_transition_probability | get_transition_probability
lineages | Lineage data
positional_mutation_prob | positional_mutation_prob
process_sequence | Generic function for process_sequence
process_sequence-method | Process sequences
prune | Generic function for prune
prune-method | prune
prune-method | prune
random_tree | random_tree
rbind-method | rbind
sample_mutation_outcome | sample_mutation_outcome
sample_mutation_site | sample_mutation_site
sample_outcome_prob | sample_outcome_prob
score_simulation | score_simulation
simulate | Generic function for simulate
simulate-method | simulate
simulate-method | simulate
simulate_core | simulate_core
sim_seqdata | sim_seqdata
substr_kmer | Generic function for substr_kmer
substr_kmer-method | Subseting a kmer_summary object
subtract | Generic function for subtract
subtract-method | subtract
subtree | Generic function for subtree
subtree-method | subtree
subtree-method | subtree
summarize_kmer | Generic function for summarize_kmer
summarize_kmer-method | summarize_kmer
summarize_kmer_core | summarize_kmer_core
WH | WH
WH_train | Train weights for WH
WH_train_fit | Train weights for WH, and output distance object