# Coordinate Covariation Analysis

## Documentation for package ‘COCOA’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

COCOA-package | Coordinate Covariation Analysis (COCOA)
aggregateLoadings | Use PCA loadings to score a region set
atf3_chr1 | Atf3 binding regions.
brcaLoadings1 | A matrix with loadings
brcaMCoord1 | A data.frame object with coordinates for cytosines from chr1 included in the PCA.
brcaMethylData1 | A matrix with DNA methylation levels from chromosome 1 for four patients.
brcaPCScores | A matrix with principal component scores for PCs 1-4 for four breast cancer patients.
brcaPCScores657 | A data.frame with principal component scores for PCs 1-4 for 657 breast cancer patients as well as a column with estrogen receptor status.
COCOA | Coordinate Covariation Analysis (COCOA)
esr1_chr1 | Estrogen receptor alpha binding regions.
gata3_chr1 | Gata3 binding regions.
getLoadingProfile | Create a "meta-region" loading profile
nrf1_chr1 | Nrf1 binding regions.
regionQuantileByPC | Visualize how individual regions are associated with principal components
rsRankingIndex | Get indices for top scored region sets
rsScoreHeatmap | Heatmap of region set scores
rsScores | Example COCOA Results (made up)
runCOCOA | Do COCOA with many region sets
signalAlongPC | Visualize how genomic signal in a region set changes along principal component axis