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

Share:

Performs the JIVE decompositions 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. 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.

Author
Michael J. O'Connell and Eric F. Lock
Date of publication
2016-07-25 10:12:01
Maintainer
Michael J. O'Connell <oconn725@umn.edu>
License
GPL-3
Version
1.7

View on CRAN

Man pages

Data
BRCA TCGA Dataset
jive
JIVE Decomposition for Multi-source Data
pjsum
Calculate Number of Free Parameters for BIC Calculation
plot.jive
Create Plots for a JIVE Object
r.jive-package
Perform JIVE Decompositions for Multi-Source Data
showHeatmaps
Heatmaps for JIVE Decompositions
show.image
Draw a Heatmap from a Matrix
showPCA
Principal Component Plots for JIVE Decomposition
showVarExplained
Display Variance Explained
SimData
Simulated Dataset
SimResults
JIVE Results for Simulated Dataset
summary.jive
Summarize a JIVE Decomposition
svdwrapper
Wrapper Function to Perform SVD

Files in this package

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