associationSignatures

Perform the estimation of the mutational signatures associated to mutations in specific genes.

associationSignatures(alterations, signatures)

Arguments

alterations

Matrix with the observed mutations (columns) for each patient (rows) as binary variables.

signatures

Matrix with the estimated exposures to signatures (columns) for each patient (rows).

Value

A list with the association estimates. It includes 6 elements: alterations: matrix with the observed mutations (columns) for each patient (rows) as binary variables. signatures: matrix with the estimated exposures to signatures (columns) for each patient (rows). associations: estimated associations. intercept: intercept resulting from the regularized regression estimate. probabilities: probability of observing a mutation in a certain gene given the presence of specific signatures. fold_changes: fold changes estimating the strength of the associations.

Examples

data(association_mutations)
set.seed(12345)
alterations = association_mutations$alterations
normalized_alpha = association_mutations$normalized_alpha
association_signatures = associationSignatures(alterations = alterations, signatures = normalized_alpha)