as.alpha                as.alpha
as.alpha.in.range       as.alpha.in.range
as.beta                 as.beta
as.beta.in.range        as.beta.in.range
as.loglik.progression   as.loglik.progression
as.loglik.progression.in.range
                        as.loglik.progression.in.range
as.mean.squared.error   as.mean.squared.error
as.starting.beta        as.starting.beta
as.starting.beta.in.range
                        as.starting.beta.in.range
background              germline replication error
cv_example              example of results obtained with the function
                        nmf.LassoCV on the counts input from
                        Nik-Zainal, Serena, et al. (2016).
evaluate.lambda.range   evaluate.lambda.range
import.counts.data      import.counts.data
lambda_range_example    example of results obtained with the function
                        evaluate.lambda.range on the counts input from
                        Nik-Zainal, Serena, et al. (2016).
mutation_categories     trinucleotides mutation categories
nmf.LassoCV             nmf.LassoCV
nmf.LassoK              nmf.LassoK
nmf_LassoK_example      example of results obtained with the function
                        nmf.LassoK on the counts input from Nik-Zainal,
                        Serena, et al. (2016).
patient.plot            patient.plot
patients                point mutations for 560 breast tumors
signatures.plot         signatures.plot
ssm560_reduced          a reduced version of the point mutations for
                        560 breast tumors in the format compatible with
                        the import function
starting.betas.estimation
                        starting.betas.estimation
starting_betas_example
                        example of results obtained with the function
                        starting.betas.estimation on the counts input
                        from Nik-Zainal, Serena, et al. (2016).
