R package for tumour phylogenetic tree reconstruction

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Documentation for package ‘CONIPHER’ version 2.1.0

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calc.pyclone.ci Function to compute confidence intervals of each cluster in each region
clonality.function Function to determine cluster clonality in each tumour region
clusterDistributionAcrossGenome Function to determine the distribution of location of mutations within a cluster
clustering_postprocess Postprocessing of clustering function
clustering_preprocess Input data preprocessing function
clustering_run Main clustering function
color.tree Plotting function to colour the nodes on the phylogenetic tree
compute_subclonal_expansion_score Function to compute subclonal expansion score on a selected alternative tree, on a tumour sample and whole tumour level. The subclonal expansion score for each tumour sample is computed as the maximum CCF of any of the terminal (leaf) nodes present in that tumour sample. Note, for multi-sample cases, there may exist a sample with no terminal nodes present, in which case the subclonal expansion score for this sample is set to 0. The tumour level subclonal expansion score is taken as the maximum subclonal expansion score across tumour samples.
compute_subclone_proportions Function to compute clone proportions on a selected alternative tree structure
compute_sum_condition_error Function to compute the Sum Condition Error for a list of trees
compute_tree_edge_probability Function to compute the edge probability score for a list of trees
conipher_clustering Full clustering run function
conipher_run Full CONIPHER run
conipher_treebuilding Full tree building run function
correct.clonality.nesting Function to correct nesting based on cluster clonality
createAllPathsList Function to create a list of all tree paths
determine.cluster.nesting Function to determine cluster nesting structure.
extract_consensus_relationships Function to take a list of trees and identify the consensus relationships
extract_daughters Function to extract all daughter clones from a parent using a phylogenetic tree
get_terminal_clusters Function to extract the terminal nodes of a phylogenetic tree
get_tree_level Function to compute the tree level of a cluster
grow.multi.trees Function to determine all possible alternative phylogenies
grow.trees Function to determine default tree structure
input_table Example input table
is.there.ccf.issue Function to check whether there is a CCF level issue
permute.clusters.to.remove Function to test which clusters are best to remove from tree This function permutes through clusters and checks which are the best to remove from the tree - takes into account number of mutations
process_mean_cluster_ccfs Function to extract the terminal nodes of a phylogenetic tree
prune.tree Function to prune the ancestral graph
remove_clustered_clones Function to remove mutation clusters with genomically clustered mutations
test.distributions Test difference in PhyloCCF distributions of each pair of mutation clusters
treebuilding_plot TRACERx tree plotting function
treebuilding_preprocess Input data preprocessing function
treebuilding_run TRACERx tree building function
unfold_tree Function to unfod tree