Man pages for COCOA
Coordinate Covariation Analysis
| 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... |
| brcaATACData1 | A matrix with ATAC-seq counts in select peak regions from... |
| brcaMCoord1 | A GRanges object with genomic coordinates for cytosines from... |
| brcaMetadata | A data.frame with patient metadata for breast cancer... |
| brcaMethylData1 | A matrix with DNA methylation levels from some CpGs on... |
| brcaPCScores | A matrix with principal component scores for PCs 1-4 for four... |
| brcaPCScores657 | A data.frame with principal component scores for PCs 1-4 for... |
| COCOA | Coordinate Covariation Analysis (COCOA) |
| convertToFromNullDist | Converts COCOA permutation results to null distributions and... |
| 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... |
| 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... |
| 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... |
