# Coordinate Covariation Analysis

## Documentation for package ‘COCOA’ version 2.26.0

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

## Help Pages

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