Coordinate Covariation Analysis

Documentation for package ‘COCOA’ version 2.6.0

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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.
COCOA	Coordinate Covariation Analysis (COCOA)
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