ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

Installation

R package ACNE is available on CRAN and can be installed in R as:

install.packages("ACNE")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/ACNE", ref="develop")

This will install the package from source.

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Version

Install

install.packages('ACNE')

Monthly Downloads

511

Version

0.9.2

License

LGPL (>= 2.1)

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Repository

https://github.com/HenrikBengtsson/ACNE

Maintainer

Henrik Bengtsson

Last Published

August 19th, 2025

Functions in ACNE (0.9.2)

Robust initialization of the W (affinity) matrix

pseudoinverse

Calculates the pseudo inverse of a matrix

robustHInit

Robust initialization of the H (copy number) matrix

NmfPlm

The NmfPlm class

fitSnpNmf

Non-negative matrix factorization (NMF) of a matrix containing SNP probe signals

removeOutliers

Removes outliers in matrix containing SNP signals

WHInit

Initialization of the W and H matrices

plot.SnpNmfFit

Generates a multi-panel plot summarizing the NMF SNP fit

fitSnpNmfArray

Allele-specific copy number estimation using non-negative matrix factorization (NMF)

snpArrayToMatrix

Reshapes SNP data in matrix form to array form and vice versa

NmfSnpPlm

The NmfSnpPlm class

Non-documented objects