SparseSignatures

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Documentation for package ‘SparseSignatures’ version 2.3.2

• 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).