Data

clusts

These data were obtained from the data freeze for The Cancer Genome Atlas flagship BRCA publication (Cancer Genome Atlas Network, 2013), and processed as described in Lock and Dunson, 2013. Gene expression, methylation, and miRNA data are provided for 348 BRCA tumor samples.

datasets

BRCA_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.

Michael J. O'Connell

r.jive

Perform JIVE Decomposition for Multi-Source Data

Eric F. Lock

Adam Kaplan

BRCA_Data function

This dataset is a list of three entries for three different molecular sources:<ul>
<li>Data[[1]] (Data$Expression): gene expression matrix for 654 genes (rows) and 348 samples (columns)</li>
<li>Data[[2]] (Data$Methylation): DNA methylation matrix for 574 cg sites (rows) and 348 samples (columns)</li>
<li>Data[[3]] (Data$miRNA): miRNA expression matrix for 423 cg sites (rows) and 348 samples (columns).</li>
</ul>The 348 columns are shared by the data sources (here, they correspond to tumor samples)

Format

BRCA TCGA Dataset — BRCA_Data

BRCA TCGA Dataset

BRCA_Data: BRCA TCGA Dataset

Description

Usage

Arguments

Format

References