Coordinate Covariation Analysis


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Documentation for package ‘COCOA’ version 1.0.2

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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