SparseSignatures


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Documentation for package ‘SparseSignatures’ version 2.6.0

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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).