startingBetaEstimation: startingBetaEstimation

In SparseSignatures: SparseSignatures

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)

SparseSignatures documentation built on Nov. 8, 2020, 4:55 p.m.