Coordinate Covariation Analysis

Documentation for package ‘COCOA’ version 1.2.0

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