# SparseSignatures

## Documentation for package ‘SparseSignatures’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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).