https://github.com/lockEF/bidifac

Bidimensional matrix factorization
https://github.com/lockEF/bidifac

Last synced: about 1 month ago
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Bidimensional matrix factorization

• Host: GitHub
• URL: https://github.com/lockEF/bidifac
• Owner: lockEF
• Created: 2018-12-10T23:17:24.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2024-04-11T01:48:57.000Z (8 months ago)
• Last Synced: 2024-08-02T20:43:39.923Z (4 months ago)
• Language: R
• Size: 55.7 KB
• Stars: 3
• Watchers: 3
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-multi-omics - BIDIFAC - Park - bidimensional integrative factorization - [paper 1](https://doi.org/10.1111/biom.13141), [paper 2](https://arxiv.org/abs/2002.02601) (Software packages and methods / Multi-omics correlation or factor analysis)

README

        
# BIDIFAC

Bidimensional matrix factorization

R code to perform factorization and dimension reduction of bidimensionally linked data matrices [1].  The file BIDIFAC.R gives functions to perform the BIDIFAC factorization, simulate data, and perform missing value imputation using BIDIFAC.  See BIDIFAC_example.R for example usage.  Written by [Jun Young Park](https://www.statisticspark.com/).  

[1] J Park and EF Lock. Integrative Factorization of Bidimensionally Linked Matrices.  Biometrics, 2019. [(article link)](https://onlinelibrary.wiley.com/doi/abs/10.1111/biom.13141) [arXiv preprint: 1906.03722](https://arxiv.org/abs/1906.03722).

The functions bidifac.plus.R, bidifac.plus.impute.R, and bidifac.plus.given.R perform the BIDIFAC+ method, described in [2].  See bidifac.plus_example.R for example usage.    

[2] EF Lock, J Park and KA Hoadley.  Bidimensional linked matrix factorization for pan-omics pan-cancer analysis,  Annals of Applied Statistics  2022.  [(article link)](https://projecteuclid.org/journals/annals-of-applied-statistics/volume-16/issue-1/Bidimensional-linked-matrix-factorization-for-pan-omics-pan-cancer-analysis/10.1214/21-AOAS1495.short)

The functions in EV_Bidifac_Functions.R perform an empirical variational Bayes version of the decompostion, as described in [3]. See EV_Bidifac_Examples.R for example usage. 

[3] Working preprint: https://ericfrazerlock.com/EVBIDI_Manuscript.pdf .