Coordinate Covariation Analysis

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Documentation for package ‘COCOA’ version 2.23.1

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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