startingBetaEstimation {SparseSignatures} | R Documentation |
Perform a robust estimation of the starting betas for the nmfLasso method
startingBetaEstimation( x, K = 3:10, background_signature = NULL, normalize_counts = TRUE, nmf_runs = 10, seed = NULL, verbose = TRUE )
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? |
A list containing the starting beta values for each configuration of K.
data(background) data(patients) res = startingBetaEstimation(x=patients[1:100,], K=3:5, background_signature=background, nmf_runs=1, seed=12345)