Tree_generation

A dataframe with cellularities (ranging from 0 to 1) of each clone (rows) in each sample (columns)

Clone_cellularities

A numeric vector giving the spatial and/or temporal distribution of the samples

timepoints

Generates a list of possible trees based on the cellularity of each clone, and the spatial and temporal distribution of the samples.
Assumption is made the different clones are on different lines of the matrix

inference

phylogeny

Clonal

Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.

Tree_generation: Phylogenetic tree

Description

Usage

Arguments