COCOA-package |
Coordinate Covariation Analysis (COCOA) |
aggregateLoadings |
Use PCA loadings to score a region set |
atf3_chr1 |
Atf3 binding regions. |
brcaLoadings1 |
A matrix with loadings |
brcaMCoord1 |
A data.frame object with coordinates for cytosines from chr1 included in the PCA. |
brcaMethylData1 |
A matrix with DNA methylation levels from chromosome 1 for four patients. |
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) |
esr1_chr1 |
Estrogen receptor alpha binding regions. |
gata3_chr1 |
Gata3 binding regions. |
getLoadingProfile |
Create a "meta-region" loading profile |
nrf1_chr1 |
Nrf1 binding regions. |
regionQuantileByPC |
Visualize how individual regions are associated with principal components |
rsRankingIndex |
Get indices for top scored region sets |
rsScoreHeatmap |
Heatmap of region set scores |
rsScores |
Example COCOA Results (made up) |
runCOCOA |
Do COCOA with many region sets |
signalAlongPC |
Visualize how genomic signal in a region set changes along principal component axis |