FLASH_main

Output from Schrodinger cellularities

Schrod_cells

One of "tree", "AIC", "BIC" or numeric. "tree" will use "ccc","ch" and "gap" methods from NbClust 
to determine the number of clusters. "BIC","AIC" or numeric values will use methods from QuantumClone.

model.selection

vector with contamination fraction in each sample

conta

vector with the number of clusters to test (alternatively only min and max values)

Nclus

tree

Dissimilarity matrix, required if model selection is "tree"

dissimMatrix

Returns number of clusters based on model selection

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.

FLASH_main: Flash core

Description

Usage

Arguments