nmfLassoCV: nmfLassoCV

In danro9685/SparseSignatures: SparseSignatures

nmfLassoCV

Description

Perform the assessment of different nmfLasso solutions by cross validation for K (unknown) somatic mutational signatures given a set of observations x. The estimation can slow down because of memory usage and intensive computations, when a big number of cross validation repetitions is asked and when the grid search is performed for a lot of configurations. In this case, an advice may be to split the computation into multiple smaller sets.

Usage

nmfLassoCV(
  x,
  K = 3:10,
  starting_beta = NULL,
  background_signature = NULL,
  normalize_counts = TRUE,
  nmf_runs = 10,
  lambda_values_alpha = c(0, 0.01, 0.05, 0.1),
  lambda_values_beta = c(0, 0.01, 0.05, 0.1),
  cross_validation_entries = 0.01,
  cross_validation_iterations = 5,
  cross_validation_repetitions = 50,
  iterations = 30,
  max_iterations_lasso = 10000,
  num_processes = Inf,
  seed = NULL,
  verbose = TRUE,
  log_file = ""
)

Arguments

x	count matrix for a set of n patients and 96 trinucleotides.
K	a range of numeric value (each of them greater than 1) indicating the number of signatures to be discovered.
starting_beta	a list of starting beta value for each configuration of K. If it is NULL, starting betas are estimated by NMF.
background_signature	background signature to be used. If not provided, a warning is thrown and an initial value for it is estimated by NMF. If beta is not NULL, this parameter is ignored.
normalize_counts	if true, the input count matrix x is normalize such that the patients have the same number of mutation.
nmf_runs	number of iteration (minimum 1) of NMF to be performed for a robust estimation of starting beta. If beta is not NULL, this parameter is ignored.
lambda_values_alpha	value of LASSO to be used for alpha between 0 and 1. This value should be greater than 0. 1 is the value of LASSO that would shrink all the signatures to 0 within one step. The higher lambda_rate_alpha is, the sparser are the resulting exposures, but too large values may result in a reduced fit of the observed counts.
lambda_values_beta	value of LASSO to be used for beta between 0 and 1. This value should be greater than 0. 1 is the value of LASSO that would shrink all the signatures to 0 within one step. The higher lambda_rate_beta is, the sparser are the resulting exposures, but too large values may result in a reduced fit of the observed counts.
cross_validation_entries	Percentage of cells in the count matrix to be replaced by 0s during cross validation.
cross_validation_iterations	For each configuration, the first time the signatures are discovered form a matrix with a percentage of values replaced by 0s. This may result in poor fit/results. Then, we perform predictions of these entries and replace them with such predicted values. This parameter is the number of restarts to be performed to improve this estimate and obtain more stable solutions.
cross_validation_repetitions	Number of time cross-validation should be repeated. Higher values result in better estimate, but are computationally more expensive.
iterations	Number of iterations to be performed. Each iteration corresponds to a first step where beta is fitted and a second step where alpha is fitted.
max_iterations_lasso	Number of maximum iterations to be performed during the sparsification via Lasso.
num_processes	Number of processes to be used during parallel execution. To execute in single process mode, this parameter needs to be set to either NA or NULL.
seed	Seed for reproducibility.
verbose	boolean; Shall I print all messages?
log_file	log file where to print outputs when using parallel. If parallel execution is disabled, this parameter is ignored.

Value

A list of 2 elements: grid_search_mse and and grid_search_loglik. Here, grid_search_mse reports the mean squared error for each configuration of performed cross validation; grid_search_loglik reports for each configuration the number of times the algorithm converged.

Examples

data(background)
data(patients)
res = nmfLassoCV(x=patients[1:100,],
     K=3:5,
     background_signature=background,
     nmf_runs=1,
     lambda_values_alpha=c(0.00),
     lambda_values_beta=c(0.00),
     cross_validation_repetitions=2,
     num_processes=NA,
     seed=12345)

danro9685/SparseSignatures documentation built on Nov. 1, 2024, 8:54 p.m.