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 nonnegative 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 volumeregularized NMF and "anchorfree" 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.
Package details 


Author  Ruslan Soldatov [aut], Peter Kharchenko [aut], Evan Biederstedt [cre, aut] 
Maintainer  Evan Biederstedt <evan.biederstedt@gmail.com> 
License  GPL3 
Version  1.0.0 
URL  https://github.com/kharchenkolab/vrnmf 
Package repository  View on CRAN 
Installation 
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