# SparseSignatures

## Documentation for package ‘SparseSignatures’ version 2.16.0

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

## Help Pages

background | germline replication error
background2 | COSMIC replication error
cv_example | example of results obtained with the function nmf.LassoCV on the counts input from Nik-Zainal, Serena, et al. (2016).
import.trinucleotides.counts | import.trinucleotides.counts
imported_data | example of imported data from Nik-Zainal, Serena, et al. (2016).
lambdaRangeAlphaEvaluation | lambdaRangeAlphaEvaluation
lambdaRangeBetaEvaluation | lambdaRangeBetaEvaluation
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
nmfLasso | nmfLasso
nmfLassoBootstrap | nmfLassoBootstrap
nmfLassoCV | nmfLassoCV
nmf_LassoK_example | example of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
patients | point mutations for 560 breast tumors
patients.plot | patients.plot
sigAssignmentCV | sigAssignmentCV
sigAssignmentEvaluation | sigAssignmentEvaluation
sigAssignmentLasso | sigAssignmentLasso
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
startingBetaEstimation | startingBetaEstimation
starting_betas_example | example of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).