startingBetaEstimation {SparseSignatures} | R Documentation

## startingBetaEstimation

### Description

Perform a robust estimation of the starting betas for the nmfLasso method

### Usage

    startingBetaEstimation(
      x,
      K = 3:10,
      background_signature = NULL,
      normalize_counts = TRUE,
      nmf_runs = 10,
      seed = NULL,
      verbose = TRUE
    )

### Arguments

`x` | count matrix for a set of n patients and 96 trinucleotides.
`K` | numeric value (minimum 2) indicating the number of signatures to be discovered.
`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.
`seed` | Seed for reproducibility.
`verbose` | boolean; Shall I print all messages?

### Value

A list containing the starting beta values for each configuration of K.

### Examples

    data(background)
    data(patients)
    res = startingBetaEstimation(x=patients[1:100,],
         K=3:5,
         background_signature=background,
         nmf_runs=1,
         seed=12345)

[Package SparseSignatures version 2.2.0 Index]