All functions

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