Compute_objective

tree

Number of clusters used for cutting (numeric of length 1)

nclus

Output from Schrodinger cellularities

Schrod

Numeric value of contamination fraction in each sample

conta

Compute the value of clustering based on same principles as QuantumClone EM

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.

Compute_objective: Compute value of objective function

Description

Usage

Arguments