nmfLassoBootstrap {SparseSignatures} | R Documentation

## 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)

[Package SparseSignatures version 2.2.0 Index]