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| 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). |
| 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). |