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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.

[1] J Park and EF Lock. Integrative Factorization of Bidimensionally Linked Matrices. <em> Biometrics</em>, 2019. (article link) arXiv preprint: 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, <em> Annals of Applied Statistics </em> 2022. (article link)

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 .