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

Performs the 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 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.

Install the latest version of this package by entering the following in R:
install.packages("r.jive")
AuthorMichael J. O'Connell and Eric F. Lock
Date of publication2017-04-12 13:41:29 UTC
MaintainerMichael J. O'Connell <oconn725@umn.edu>
LicenseGPL-3
Version2.1

View on CRAN

Files

inst
inst/doc
inst/doc/BRCA_Example.html
inst/doc/BRCA_Example.Rmd
NAMESPACE
data
data/BRCA_data.rda
data/datalist
data/SimResults.rda
data/SimData.rda
R
R/jive.r R/showHeatmaps.r R/showVarExplained.r R/jive.predict.r R/showPCA.r
vignettes
vignettes/HeatmapsBRCA.png
vignettes/HeatmapIndivMeth.png
vignettes/JointPCA.png
vignettes/BRCA_Example.Rmd
vignettes/MorePCA.png
vignettes/VarExplained.png
vignettes/rjive_bib.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/SimData.Rd man/summary.jive.Rd man/jive.Rd man/showPCA.Rd man/jive.predict.Rd man/SimResults.Rd man/show.image.Rd man/Data.Rd man/showHeatmaps.Rd man/svdwrapper.Rd man/showVarExplained.Rd man/r.jive-package.Rd man/pjsum.Rd man/plot.jive.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.