mutation_assignment_em: Assign mutations for multi-dimensional clustering by adding...

In Wedge-Oxford/dpclust: DPClust - An R package for subclonal reconstruction of tumours using sequencing data

Assign mutations for multi-dimensional clustering by adding clusters until the likelihood no longer improves

Description

Assign mutations for multi-dimensional clustering by adding clusters until the likelihood no longer improves

Usage

mutation_assignment_em(GS.data, mutCount, WTCount, subclonal.fraction,
  node.assignments, opts)

Arguments

GS.data	Output from the MCMC chain
mutCount	Matrix containing counts of the mutated allele
WTCount	Matrix containing counts of the wild type allele
subclonal.fraction	Matrix with cancer cell fraction estimates for each mutation in each sample
node.assignments	Matrix with assignments of mutations to clusters during MCMC (i.e. GS.data$S.i)
opts	List with various parameters, including samplename and number of iterations

Value

Standardised clustering output, including mutation assignments, likelihoods and cluster positions

Author(s)

dw9, sd11

Wedge-Oxford/dpclust documentation built on July 6, 2024, 2:02 p.m.