SparseSignatures


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Documentation for package ‘SparseSignatures’ version 1.0.3

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as.alpha as.alpha
as.alpha.in.range as.alpha.in.range
as.beta as.beta
as.beta.in.range as.beta.in.range
as.loglik.progression as.loglik.progression
as.loglik.progression.in.range as.loglik.progression.in.range
as.mean.squared.error as.mean.squared.error
as.starting.beta as.starting.beta
as.starting.beta.in.range as.starting.beta.in.range
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).
evaluate.lambda.range evaluate.lambda.range
import.counts.data import.counts.data
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
nmf.LassoCV nmf.LassoCV
nmf.LassoK nmf.LassoK
nmf_LassoK_example example of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
patient.plot patient.plot
patients point mutations for 560 breast tumors
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
starting.betas.estimation starting.betas.estimation
starting_betas_example example of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).