tempoSig-class: Class 'tempoSig' for storing catalog and exposure

In mskcc/tempoSig: Maximum Likelihood Fitting of Mutational Catalogs and De Novo Inference of Signatures

Class tempoSig for storing catalog and exposure

Description

S4 class with storage for input catalog, reference signatures, and output exposure inferred.

Value

Object of class tempoSig

Slots

catalog

Matrix of mutation count with samples in columns and mutation types in rows

signat

Matrix of reference signatures; each column stores individual signatures proportions with mutation types in rows

tmb

Vector of total mutation loads for each sample

expos

Matrix of inferred proportions of signatures exposure; each row gives proportions of each sample with signatures in columns

pvalue

P-values of exposures estimated from permutation tests; same dimension as expos

logLik

Log likelihood

misc

List of factorization results and measures for de novo runs

mskcc/tempoSig documentation built on Feb. 3, 2023, 8:35 a.m.