vrnmf: Volume-Regularized Structured Matrix Factorization

Implements a set of routines to perform structured matrix factorization with minimum volume constraints. The NMF procedure decomposes a matrix X into a product C * D. Given conditions such that the matrix C is non-negative and has sufficiently spread columns, then volume minimization of a matrix D delivers a correct and unique, up to a scale and permutation, solution (C, D). This package provides both an implementation of volume-regularized NMF and "anchor-free" NMF, whereby the standard NMF problem is reformulated in the covariance domain. This algorithm was applied in Vladimir B. Seplyarskiy Ruslan A. Soldatov, et al. "Population sequencing data reveal a compendium of mutational processes in the human germ line". Science, 12 Aug 2021. <doi:10.1126/science.aba7408>. This package interacts with data available through the 'simulatedNMF' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/vrnmf>. The size of the 'simulatedNMF' package is approximately 8 MB.

Getting started

Package details

AuthorRuslan Soldatov [aut], Peter Kharchenko [aut], Evan Biederstedt [cre, aut]
MaintainerEvan Biederstedt <evan.biederstedt@gmail.com>
LicenseGPL-3
Version1.0.0
URL https://github.com/kharchenkolab/vrnmf
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("vrnmf")

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vrnmf documentation built on Aug. 20, 2021, 5:07 p.m.