m.step: Maximization step

Description Usage Arguments

View source: R/EM.R

Description

Optimization of clone positions and proportion of mutations in each clone, based on the previously calculated expectation

Usage

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m.step(fik, Schrod, previous.weights, previous.centers, contamination,
  adj.factor, optim = "default")

Arguments

fik

Matrix giving the probability of each mutation to belong to a specific clone

Schrod

A list of dataframes (one for each sample), generated by the Patient_schrodinger_cellularities() function.

previous.weights

Weights from the previous optimization step (used as priors for this step)

previous.centers

Clone coordinates from previous optimization step (used as priors for this step)

contamination

Numeric vector with the fraction of normal cells contaminating the sample

adj.factor

Factor to compute the probability: makes transition between the cellularity of the clone and the frequency observed

optim

use L-BFS-G optimization from R ("default"), or from optimx ("optimx"), or Differential Evolution ("DEoptim")


QuantumClone documentation built on May 2, 2019, 3:03 a.m.