r.jive: Perform JIVE Decomposition for Multi-Source Data

Performs the Joint and Individual Variation Explained (JIVE) decomposition on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data [O'Connell, MJ and Lock, EF (2016) <doi:10.1093/bioinformatics/btw324>]. It provides two methods of rank selection when the rank is unknown, a permutation test and a Bayesian Information Criterion (BIC) selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.

Version:	2.4
Depends:	R (≥ 2.10.0)
Imports:	gplots, abind, graphics, stats
Suggests:	knitr, rmarkdown
Published:	2020-11-17
Author:	Michael J. O'Connell [aut, cre], Eric F. Lock [aut], Adam Kaplan [ctb]
Maintainer:	Michael J. O'Connell <oconnemj at miamioh.edu>
License:	GPL-3
NeedsCompilation:	no
CRAN checks:	r.jive results

Documentation:

Reference manual:	r.jive.pdf
Vignettes:	Example with TCGA Data

Downloads:

Package source:	r.jive_2.4.tar.gz
Windows binaries:	r-devel: r.jive_2.4.zip, r-release: r.jive_2.4.zip, r-oldrel: r.jive_2.4.zip
macOS binaries:	r-release (arm64): r.jive_2.4.tgz, r-oldrel (arm64): r.jive_2.4.tgz, r-release (x86_64): r.jive_2.4.tgz, r-oldrel (x86_64): r.jive_2.4.tgz
Old sources:	r.jive archive

Reverse dependencies:

Reverse suggests:

multiblock

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