nmfLassoBootstrap: nmfLassoBootstrap

In danro9685/SparseSignatures: SparseSignatures

nmfLassoBootstrap

Description

Perform the evaluation of different nmfLasso solutions by bootstrap 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 bootstrap repetitions is asked and when the analysis is performed for a big range of signatures (K). In this case, an advice may be to split the computation into multiple smaller sets.

Usage

nmfLassoBootstrap(
  x,
  K = 3:10,
  starting_beta = NULL,
  background_signature = NULL,
  normalize_counts = TRUE,
  nmf_runs = 10,
  bootstrap_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.
bootstrap_repetitions	Number of time bootstrap 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 3 elements: stability, RSS and evar. Here, stability reports the estimared cosine similarity for alpha and beta at each bootstrap repetition; RSS reports for each configuration the estimated residual sum of squares; finally, evar reports the explained variance.

Examples

data(background)
data(patients)
res = nmfLassoBootstrap(x=patients[1:100,],
     K=3:5,
     background_signature=background,
     nmf_runs=1,
     bootstrap_repetitions=2,
     num_processes=NA,
     seed=12345)

danro9685/SparseSignatures documentation built on April 29, 2024, 2:21 a.m.