COCOA                   Coordinate Covariation Analysis (COCOA)
aggregateSignal         Score a region set using feature contribution
                        scores
aggregateSignalGRList   Score many region sets
atf3_chr1               Atf3 binding regions.
brcaATACCoord1          A GRanges object with coordinates for select
                        BRCA ATAC-seq peak regions from chr1.
brcaATACData1           A matrix with ATAC-seq counts in select peak
                        regions from chromosome 1 for 37 patients.
brcaMCoord1             A GRanges object with genomic coordinates for
                        cytosines from chr1 for the package's built-in
                        DNA methylation data
brcaMetadata            A data.frame with patient metadata for breast
                        cancer patients.
brcaMethylData1         A matrix with DNA methylation levels from some
                        CpGs on chromosome 1
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.
convertToFromNullDist   Converts COCOA permutation results to null
                        distributions and vice versa
esr1_chr1               Estrogen receptor alpha binding regions.
gata3_chr1              Gata3 binding regions.
getGammaPVal            Get a p-value for region set scores based on a
                        gamma distribution.
getMetaRegionProfile    Create a "meta-region" profile
getPermStat             Get p-value or z-score based on permutation
                        results
getTopRegions           Get regions that are most associated with
                        target variable
nrf1_chr1               Nrf1 binding regions.
plotAnnoScoreDist       Plot ranked region set scores, annotating
                        groups of interest
regionQuantileByTargetVar
                        Visualize how individual regions are associated
                        with target variable
rsRankingIndex          Get indices for top scored region sets
rsScoreHeatmap          Heatmap of region set scores
rsScores                Example COCOA Results (made up)
runCOCOA                Run COCOA: quantify inter-sample variation,
                        score region sets
runCOCOAPerm            Run COCOA permutations to get p-values
signalAlongAxis         Visualize how genomic signal in a region set
                        changes along a given axis
