Package index • SparseSignatures

All functions
`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).

Reference