Cluster_plot_from_cell: Cellularity clustering

Description Usage Arguments

View source: R/QuantumClone.R

Description

Clustering cellularities based on the most likely presence of a clone, using the pamk algorithm (fpc package). Clustering can be guided by toggling manual_clustering on and/or giving a range of number of clusters.

Usage

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Cluster_plot_from_cell(Cell, Sample_names, simulated, save_plot = TRUE,
  contamination, clone_priors, prior_weight, nclone_range, Initializations,
  preclustering = TRUE, epsilon = 5 * (10^(-3)), ncores = 2,
  output_directory = NULL, model.selection = "BIC", optim = "default",
  keep.all.models = FALSE)

Arguments

Cell

Output from Return_one_cell_by_mut, list of cellularities (one list-element per sample)

Sample_names

Name of the sample

simulated

Was the data generated by QuantumCat?

save_plot

Should the clustering plots be saved? Default is True

contamination

The fraction of normal cells in the samples

clone_priors

If known a list of priors (cell prevalence) to be used in the clustering

prior_weight

If known a list of priors (fraction of mutations in a clone) to be used in the clustering

nclone_range

Number of clusters to look for

Initializations

Maximal number of independant initial condition tests to be tried

preclustering

The type of preclustering used for priors: "Flash","kmedoid" or NULL. NULL will generate centers using uniform distribution.

epsilon

Stop value: maximal admitted value of the difference in cluster position and weights between two optimization steps.

ncores

Number of CPUs to be used

output_directory

Directory in which to save results

model.selection

The function to minimize for the model selection: can be "AIC", "BIC", or numeric. In numeric, the function uses a variant of the BIC by multiplication of the k*ln(n) factor. If >1, it will select models with lower complexity.

optim

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

keep.all.models

Should the function output the best model (default; FALSE), or all models tested (if set to true)


QuantumClone documentation built on Nov. 17, 2017, 5:24 a.m.