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vrnmf
View on CRAN: Click
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Download and install vrnmf package within the R console
Install from CRAN:
install.packages("vrnmf")
Install from Github:
library("remotes")
install_github("cran/vrnmf")
Install by package version:
library("remotes")
install_version("vrnmf", "1.0.2")
Attach the package and use:
library("vrnmf")
Maintained by
Evan Biederstedt
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-08-20
Latest Update: 2022-02-25
Description:
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.
How to cite:
Evan Biederstedt (2021). vrnmf: Volume-Regularized Structured Matrix Factorization. R package version 1.0.2, https://cran.r-project.org/web/packages/vrnmf
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Some associated functions: AnchorFree . factor_intensities . infer_intensities . projection_onto_simplex . sim_factors . vol_preprocess . volnmf_det . volnmf_estimate . volnmf_logdet . volnmf_main . volnmf_procrustes . volnmf_simplex_col . volnmf_simplex_row .
Some associated R codes: anchor.R . infer_intensities.R . simulate_factorization.R . update_simplex.R . update_unitary.R . update_volume.R . volnmf_estimate.R . vpreprocess.R . Full vrnmf package functions and examples
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